@conference{jpredurl, author = {JPRED}, year = {}, title = {Jpred Distrubution Material: Http://Www.Compbio.Dundee.Ac.Uk/$\sim$Www-Jpred/Data/}, booktitle = {}, location = {}, pages = {} } @conference{swurl, author = {Stephen White's Membrane Protein Resource Page}, year = {}, title = {http://blanco.biomol.uci.edu/Membrane\_Proteins\_xtal.html}, } @conference{gpcrurl, author = {GPCRDB}, year = {}, title = {http://www.gpcr.org/} } @conference{pdburl, author = {Protein Data Bank}, year = {}, title = {http://www.rcsb.org/pdb/}, } @conference{swissproturl, author = {Swiss-Prot}, year = {}, title = {http://us.expasy.org/sprot/}, } @conference{pfamurl, author = {Pfam}, year = {}, title = {http://pfam.wustl.edu/}, } @conference{gobindgroupurl, author = {H Gobind Khorana Group}, title = {http://web.mit.edu/biology/www/facultyareas/facresearch/khorana.shtml}, year = {} } @conference{klein-seetharamangroupurl, author = {Judith Klein-Seetharaman Group}, title = {http://www.cs.cmu.edu/judithks}, year = {} } @conference{schwalbegroupurl, author = {Harald Schwalbe Group}, title = {http://schwalbe.org.chemie.uni-frankfurt.de/}, year = {} } @conference{gsgroupurl, author = {Gebhard Schertler Group}, title = {http://www2.mrc-lmb.cam.ac.uk/SS/Schertler\_G/group/}, years = {} } @misc{Anonymous, author = {Anonymous}, year = {}, title = {Biological Language Modeling Project: http://www.cs.cmu.edu/$\sim$blmt/}, } @misc{Altschul1990, author = {Altschul, SF and Gish, W and Miller, W and Myers, EW and Lipman, DJ}, year = {1990}, title = {Basic Local Alignment Search Tool}, } @book{Addison2002, author = {Addison, PS}, title = {The illustrated wavelet transmform handbook}, year = {2002}, publisher = {Institute of Physics Publishing}, place = {Bristol and Philadelphia} } @article{Andrew2001, author = {Andrew, CD and Penel, S and Jones, GR and Doig, AJ}, year = {2001}, title = {Stabilizing Nonpolar/Polar Side-Chain Interactions in the Alpha-Helix}, journal = {Proteins}, volume = {45}, issue = {4}, pages = {449-55} } @article{Arai2004, author = {Arai, M and Mitsuke, H and Ikeda, M and Xia, JX and Kikuchi, T and Satake, M and Shimizu, T}, year = {2004}, title = {Conpred Ii: A Consensus Prediction Method for Obtaining Transmembrane Topology Models with High Reliability}, journal = {Nucleic Acids Res}, volume = {32}, issue = {Web Server Issue}, pages = {W390-W393} } @ARTICLE{Baker1975, AUTHOR = {Baker, JK}, TITLE = {The Dragon System - An Overview}, JOURNAL = {IEEE Transactions on Acoustics, Speech and Signal Processing}, YEAR = {1975}, volume = {23}, number = {1}, pages = {24-29}, } @article{Baker2001, author = {Baker, D and Sali, A}, year = {2001}, title = {Protein Structure Prediction and Structural Genomics}, journal = {Science}, volume = {294}, issue = {5540}, pages = {93-6} } @book{Baldi1998, author = {Baldi, P}, year = {1998}, title = {Bioinformatics}, publisher = {MIT Press} } @article{Barril2004, author = {Barril, X and Hubbard, RE and Morley, SD}, title = {Virtual screening in structure-based drug discovery}, year = 2004, journal = {Mini Rev Med Chem}, volume = {4}, issue = {7}, pages = {779-91} } @book{Baxevanis1998, author = {Baxevanis, AD and Ouellette, BFF}, year = {1998}, title = {Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins.}, publisher = {Wiley-Interscience} } @misc{Bejerano2001, author = {Bejerano, G and Yona, G}, year = {2001}, title = {Variations on Probabilistic Suffix Trees: Statistical Modeling and Prediction of Protein Families}, } @article{Bellegarda2000, author = {Bellegarda, J}, year = {2000}, title = {Exploiting Latent Semantic Information in Statistical Language Modeling}, journal = {Proceedings of the IEEE}, volume = {88}, issue = {8}, pages = {1279-96} } @article{Bennasroune2004, author = {Bennasroune, A and Gardin, A and Aunis, D and Cremel, G and Hubert, P}, title = {Tyrosine kinase receptors as attractive targets of cancer therapy}, year = 2004, journal = {Crit Rev Oncol Hematol}, volume = 50, issue = 1, pages = {23-38} } @article{Berman1994, author = {Berman, AL, Kolker, E and Trifonov, EN}, year = {1994}, title = {Underlying Order in Protein Sequence Organization}, journal = {Proc Natl Acad Sci U S A}, volume = {91}, issue = {9}, pages = {4044-7} } @book{Berry1999, author = {Berry, MW and Browne, M}, year = {1999}, title = {Understanding Search Engines: Mathematical Modeling and Text Retrieval}, publisher = {Soc for Industrial \& Applied Math} } @article{Beuming2004, author = {Beuming, T and Weinstein, H}, year = {2004}, title = {A Knowledge-Based Scale for the Analysis and Prediction of Buried and Exposed Faces of Transmembrane Domain Proteins}, journal = {Bioinformatics}, volume = {88}, issue = {8}, pages = {1279-96} } @article{Bhattacharyya2002, author = {Bhattacharyya, R and Samanta, U and Chakrabarti, P}, year = {2002}, title = {Aromatic-Aromatic Interactions in and around Alpha-Helices}, journal = {Protein Eng}, volume = {15}, issue = {2}, pages = {91-100} } @misc{Bishop1975, author = {Bishop, YMM and Fienberg, SE and Holland, PW}, year = {1975}, title = {Discrete Multivariate Analysis} , } @article{Blaisdell1996, author = {Blaisdell, BE, Campbell, AM and Karlin, S}, year = {1996}, title = {Similarities and Dissimilarities of Phage Genomes}, journal = {Proc Natl Acad Sci U S A}, volume = {93}, issue = {12}, pages = {5854-9} } @article{Bolshoy2003, author = {Bolshoy, A}, year = {2003}, title = {DNA Sequence Analysis Linguistic Tools: Contrast Vocabularies, Compositional Spectra and Linguistic Complexity}, journal = {Appl Bioinformatics}, volume = {2}, issue = {2}, pages = {103-12} } @article{Bolshoy1997, author = {Bolshoy, A and Shapiro, K and Trifonov, E and Ioshikhes, I}, year = {1997}, title = {Enhancement of the Nucleosomal Pattern in Sequences of Lower Complexity}, journal = {Nucl. Acids. Res.}, volume = {25}, issue = {16}, pages = {3248-54} } @article{Botstein1997, author = {Botstein, D and Cherry, JM}, title = {Molecular linguistics: extracting information from gene and protein sequences}, year = {1997}, journal = {Proc Natl Acad Sci U S A}, volume = {94}, issue = {11}, pages = {5506-7} } @article{Brendel1994, author = {Brendel, V and Karlin, S}, year = {1994}, title = {Applications of Statistical Criteria in Protein Sequence Analysis: Case Study of Yeast Rna Polymerase Ii Subunits}, journal = {Comput Chem}, volume = {18}, issue = {3}, pages = {251-3} } @ARTICLE{Bull1974, AUTHOR = {Bull, HB and Breese, K}, TITLE = {Surface tension of amino acid solutions: a hydrophobicity scale of the amino acid residues}, JOURNAL = {Arch Biochem Biophys}, YEAR = {1974}, volume = {16}, number = {2}, pages = {665-670} } @article{Burge1992, author = {Burge, C, Campbell, AM and Karlin, S}, year = {1992}, title = {Over- and under-Representation of Short Oligonucleotides in DNA Sequences}, journal = {Proc Natl Acad Sci U S A}, volume = {89}, issue = {4}, pages = {1358-62} } @misc{Burge1997, author = {Burge, C and Karlin, S}, year = {1997}, title = {Prediction of Complete Gene Structures in Human Genomic DNA} } @article{Bussemaker2000, author = {Bussemaker, HJ and Li, H and Siggia, ED}, year = {2000}, title = {Building a Dictionary for Genomes: Identification of Presumptive Regulatory Sites by Statistical Analysis}, journal = {Proc Natl Acad Sci U S A}, volume = {97}, issue = {18}, pages = {10096-100} } @conference{Cai2000, author = {Cai, C and Rosenfeld, R and Wasserman, L}, year = {2000}, title = {Exponential Language Models, Logistic Regression, and Semantic Coherence}, booktitle = {Proc. NIST/DARPA Speech Transcription Workshop}, location = {}, pages = {10096-100} } @ARTICLE{Cid1992, AUTHOR = {Cid, H and Bunster, M and Canales, M and Gazitua, F}, TITLE = {Hydrophobicity and structural classes in proteins}, JOURNAL = {Protein Engineering}, YEAR = {1992}, volume = {5}, number = {5}, pages = {373-375} } @article{Landauer1997, author = {Landauer, TK and Dumais, ST}, title = {A solution to Plato's problem: TheLatent Semantic Analysis theory of acquisition, induction andrepresentation of knowledge}, year = {1997}, volume = {104}, pages = {211-240} } @article{Collado-Vides1989, author = {Collado-Vides, J}, year = {1989}, title = {A Transformational-Grammar Approach to the Study of the Regulation of Gene Expression}, journal = {J Theor Biol}, volume = {136}, issue = {4}, pages = {403-25} } @article{Collado-Vides1991, author = {Collado-Vides, J}, year = {1991}, title = {The Search for a Grammatical Theory of Gene Regulation Is Formally Justified by Showing the Inadequacy of Context-Free Grammars}, journal = {Comput Appl Biosci}, volume = {7}, issue = {3}, pages = {321-6} } @article{Collado-Vides1991b, author = {Collado-Vides, J}, year = {1991}, title = {A Syntactic Representation of Units of Genetic Information--a Syntax of Units of Genetic Information}, journal = {J Theor Biol}, volume = {148}, issue = {3}, pages = {401-29} } @article{Collado-Vides1991c, author = {Collado-Vides, J, Magasanik, B and Gralla, JD}, year = {1991}, title = {Control Site Location and Transcriptional Regulation in Escherichia Coli}, journal = {Microbiol Rev}, volume = {55}, issue = {3}, pages = {371-94} } @article{Collado-Vides1992, author = {Collado-Vides, J}, year = {1992}, title = {Grammatical Model of the Regulation of Gene Expression}, journal = {Proc Natl Acad Sci U S A}, volume = {89}, issue = {20}, pages = {9405-9} } @article{Collado-Vides1993, author = {Collado-Vides, J}, year = {1993}, title = {The Elements for a Classification of Units of Genetic Information with a Combinatorial Component}, journal = {J Theor Biol}, volume = {163}, issue = {4}, pages = {527-48} } @article{Collado-Vides1993b, author = {Collado-Vides, J}, year = {1993}, title = {A Linguistic Representation of the Regulation of Transcription Initiation. I. An Ordered Array of Complex Symbols with Distinctive Features}, journal = {Biosystems}, volume = {29}, issue = {2-3}, pages = {87-104} } @article{Collado-Vides1993c, author = {Collado-Vides, J}, year = {1993}, title = {A Linguistic Representation of the Regulation of Transcription Initiation. Ii. Distinctive Features of Sigma 70 Promoters and Their Regulatory Binding Sites}, journal = {Biosystems}, volume = {29}, issue = {2-3}, pages = {105-28} } @article{Collado-Vides1996, author = {Collado-Vides, J}, year = {1996}, title = {Towards a Unified Grammatical Model of Sigma 70 and Sigma 54 Bacterial Promoters}, journal = {Biochimie}, volume = {78}, issue = {5}, pages = {351-63} } @article{Cowan1995, author = {Cowan, SW and Garavito, RM and Jansonius, JN and Jenkins, JA and Karlsson, R and Konig, N and Pai, EF and Pauptit, RA and Rizkallah, PJ and Rosenbusch, JP}, title = {The structure of OmpF porin in a tetragonal crystal form}, year = {1995}, journal = {Structure}, volume = {3}, issue = 10, pages = {1041-50} } @article{Cowan1992, author = {Cowan, SW and Schirmer, T and Rummel, G and Steiert, M and Ghosh, R and Pauptit, RA and Jansonius, JN and Rosenbusch, JP}, title = {Crystal structures explain functional properties of two E. coli porins},year = {1992},journal = {Nature}, volume = {358}, issue = 6389, pages = {727-33}} @article{Bigelow2004, author = {Bigelow, HR and Petrey, DS and Liu, J and Przybylski, D and Rost, B}, title = {Predicting transmembrane beta-barrels in proteomes},year = {2004},journal = {Nucleic Acids Res}, volume = {32}, issue = 8, pages = {2566-77}} @article{Gromiha2004, author = {Gromiha, MM and Ahmad, S and Suwa, M}, title = {Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins},year = {2004},journal = {J Comput Chem}, volume = {25}, issue = 5, pages = {762-7}} @article{Mitaku2002, author = {Mitaku, S and Hirokawa, T and Tsuji, T}, title = {Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces},year = {2002},journal = {Bioinformatics}, volume = {18}, issue = 4, pages = {608-16}} @article{Penel1999, author = {Penel, S and Morrison, RG and Mortishire-Smith, RJ and Doig, AJ}, title = {Periodicity in alpha-helix lengths and C-capping preferences},year = {1999},journal = {J Mol Biol}, volume = {293}, issue = 5, pages = {1211-9}} @article{Eilers2002, author = {Eilers, M and Patel, AB and Liu, W and Smith, SO}, title = {Comparison of helix interactions in membrane and soluble alpha-bundle proteins},year = {2002},journal = {Biophys J}, volume = {82}, issue = 5, pages = {2720-36}} @article{Liu2004JMB, author = {Liu, W and Eilers, M and Patel, AB and Smith, SO}, title = {Helix packing moments reveal diversity and conservation in membrane protein structure},year = {2004},journal = {J Mol Biol}, volume = {337}, issue = 3, pages = {713-29}} @article{Javadpour1999, author = {Javadpour, MM and Eilers, M and Groesbeek, M and Smith, SO}, title = {Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association}, tear = {1999},journal = {Biophys J}, volume = {77}, issue = 3, pages = {1609-18}} @article{Beuming2004, author = {Beuming, T and Weinstein, H}, title = {A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins}, year = {2004}, journal = {Bioinformatics}, volume = {20}, issue = 12, pages = {1822-35} } @article{Pilpel1999, author = {Pilpel, Y and Ben-Tal, N and Lancet, D}, title = {kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction},year = {1999},journal = {J Mol Biol}, volume = {294}, issue = 4, pages = {921-35}} @article{Zhou2000, author = {Zhou, X and Alber, F and Folkers, G and Gonnet, GH and Chelvanayagam, G}, title = {An analysis of the helix-to-strand transition between peptides with identical sequence},year = {2000},journal = {Proteins}, volume = {41}, issue = 2, pages = {248-56}} @article{Kuznetsov2003, author = {Kuznetsov, IB and Rackovsky, S}, title = {On the properties and sequence context of structurally ambivalent fragments in proteins},year = {2003},journal = {Protein Sci}, volume = {12}, issue = 11, pages = {2420-33}} @book{Branden1999, author = {Carl-Ivar Branden and John Tooze}, year = {1999}, title = {Introduction to Protein Structure}, publisher = {Garland Publishing} } @conference{Cai2000, author = {Cai, C and Rosenfeld, R and Wasserman, L}, title = {Exponential Language Models, Logistic Regression, and Semantic Coherence}, booktitle = {Proc. NIST/DARPA Speech Transcription Workshop}, year = {2000} } @article{Chatzidimitriou-Dreismann1996, author = {Chatzidimitriou-Dreismann, CA and Streffer, RM and Larhammar, D}, year = {1996}, title = {Lack of Biological Significance in the 'Linguistic Features' of Noncoding DNA--a Quantitative Analysis}, journal = {Nucleic Acids Res}, volume = {24}, issue = {9}, pages = {1676-81.} } @conference{Chen1996, author = {Chen, SF and Goodman, J}, year = {1996}, title = {An Emirical Study of Smoothing Techniques for Language Modeling}, booktitle = {ACL96: Proceedings of the 34th conference on Association for Computational Linguistics}, location = {}, pages = {1676-81.} } @article{Chen2002, author = {Chen, CP and Kernytsky, A and Rost, B}, title = {Transmembrane helix predictions revisited}, year = {2002}, journal = {Protein Sci}, volume = {11}, issue = {12}, pages = {2774-91} } @conference{Cheng2004, author = {Cheng, B and Carbonell, J and Klein-Seetharaman, J}, year = {2004}, title = {A Machine Text-Inspired Machine Learning Approach for Identification of Transmembrane Helix Boundaries}, confname = {15th International Symposium on Methodologies for Intelligent Systems, Saratoga Springs}, location = , pages = {349-58} } @article{Cheng2005, author = {Cheng, B and Carbonell, J and Klein-Seetharaman, J}, year = {2005}, title = {Protein Classification Based on Text Document Classification Techniques}, journal = {Proteins - Structure, Function and Bioinformatics}, volume = {58}, issue = {4}, pages = {955-70} } @article{Chou1978, author = {Chou, PY and Fasman, GD}, year = {1978}, title = {Prediction of the Secondary Structure of Proteins from Their Amino Acid Sequence}, journal = {Adv Enzymol Relat Areas Mol Biol}, volume = {47}, issue = {9}, pages = {45-148} } @article{Clarkson1997, author = {Clarkson, PR and Rosenfeld, R}, year = {1997}, title = {Statistical Language Modeling Using the Cmu-Cambridge Toolkit.}, journal = {Proceedings ESCA Eurospeech}, volume = {47}, issue = {9}, pages = {45-148} } @misc{Coin2003, author = {Coin, L and Bateman, A and Durbin, R}, year = {2003}, title = {Enhanced Protein Domain Discovery by Using Language Modeling Techniques from Speech Recognition} , } @article{Collins1992, author = {Collins, S and Lohse, MJ and O'Dowd, B and Caron, MG and Lefkowitz, RJ}, title = {Structure and regulation of G protein-coupled receptors: the beta 2-adrenergic receptor as a model}, journal = {Vitam Horm}, year = {1991}, volume = {46}, pages = {1-39} } @article{Cserzo2004, author = {Cserzo, M and Eisenhaber, F and Eisenhaber, B and Simon, I}, year = {2004}, title = {Tm or Not Tm: Transmembrane Protein Prediction with Low False Positive Rate Using Das-Tmfilter}, journal = {Bioinformatics}, volume = {20}, issue = {1}, pages = {136-7} } @article{Cserzo1997, author = {Cserzo, M and Wallin, E and Simon, I and von Heijne, G and Elofsson, A}, year = {1997}, title = {Prediction of Transmembrane Alpha-Helices in Prokaryotic Membrane Proteins: The Dense Alignment Surface Method}, journal = {Protein Eng}, volume = {10}, issue = {6}, pages = {673-6} } @article{Cuff1998, author = {Cuff, JA and Clamp, ME and Siddiqui, AS and Finlay, M and Barton, GJ}, year = {1998}, title = {Jpred: A Consensus Secondary Structure Prediction Server}, journal = {Bioinformatics}, volume = {14}, issue = {10}, pages = {892-3} } @article{Czirok1995, author = {Czirok, A, Mantegna, RN, Havlin, S and Stanley, HE}, year = {1995}, title = {Correlations in Binary Sequences and a Generalized Zipf Analysis}, journal = {Physical Review. E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, volume = {52}, issue = {1}, pages = {446-452.} } @article{Das2000, author = {Das, R and Gerstein, M}, year = {2000}, title = {The Stability of Thermophilic Proteins: A Study Based on Comprehensice Genome Comparison}, journal = {Functional and Integrative Genomics}, volume = {52}, issue = {1}, pages = {446-452.} } @article{delaCruz2002, author = {de la Cruz, X and Hutchinson, EG and Shepherd, A and Thornton, JM}, year = {2002}, title = {Toward Predicting Protein Topology: An Approach to Identifying Beta Hairpins}, journal = {Proc Natl Acad Sci U S A}, volume = {99}, issue = {17}, pages = {11157-62} } @article{Deber2001, author = {Deber, CM and Wang, C and Liu, LP and Prior, AS and Agrawal, S and Muskat, BL and Cuticchia, AJ}, year = {2001}, title = {Tm Finder: A Prediction Program for Transmembrane Protein Segments Using a Combination of Hydrophobicity and Nonpolar Phase Helicity Scales}, journal = {Protein Sci}, volume = {10}, issue = {1}, pages = {212-9} } @article{Deerwester1990, author = {Deerwester, S}, year = {1990}, title = {Indexing by Latent Semantic Analysis}, journal = {J American Society of Information Processing}, volume = {10}, issue = {1}, pages = {212-9} } @misc{Delcher1999, author = {Delcher, AL and Kasif, S and Fleischmann, RD and Peterson, J and White, O and Salzberg, SL}, year = {1999}, title = {Alignment of Whole Genomes} } @book{Deller1999, author = {Deller, JR and Hansen, JHL and Proakis, JG}, year = {1999}, title = {Discrete-Time Processing of Speech Signals}, publisher = {Wiley-IEEE press} } @article{Dong1994, author = {Dong, S and Searls, DB}, year = {1994}, title = {Gene Structure Prediction by Linguistic Methods}, journal = {Genomics}, volume = {23}, issue = {3}, pages = {540-51} } @inproceedings{Dong2005, author = {Dong, QW and Lin, L and Wang, XL}, title = {A Pattern-Based SVM for Protein Remote Homology Detection}, year = {2005}, journal = {Machine Learning and Cybernetics}, volume = {6}, pages = {3363- 3368} } @article{Dong2006, author = {Dong, QW and Wang, XL and Lin, L}, title = {Application of latent semantic analysis to protein remote homology detection}, year = {2006}, journal = {Bioinformatics}, volume = {22}, issue = {3}, pages = {285-90} } @misc{Dorohonceanu2000, author = {Dorohonceanu, B and Nevill-Manning, CG}, year = {2000}, title = {Accelerating Protein Classification Using Suffix Trees} , } @misc{Durbin1998, author = {Durbin, R and Eddy, S and Krogh, A and Mitchison, G}, year = {1998}, title = {Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids} } @article{Dwyer2001, author = {Dwyer, DS}, year = {2001}, title = {Electronic Properties of the Amino Acid Side Chains Contribute to the Structural Preferences in Protein Folding}, journal = {J Biomol Struct Dyn}, volume = {18}, issue = {6}, pages = {881-92} } @article{Efremov2004, author = {Efremov, RG and Nolde, DE and Konshina, AG and Syrtcev, NP and Arseniev AS}, title = {Peptides and proteins in membranes: what can we learn via computer simulations?}, journal = {Curr Med Chem}, year = {2004}, volume = {1}, issue = {18}, pages = {2421-42} } @article{Eisenberg1982, author = {Eisenberg, D and Weiss, RM and Terwilliger, TC}, year = {1982}, title = {The Helical Hydrophobic Moment: A Measure of the Amphiphilicity of a Helix}, journal = {Nature}, volume = {299}, issue = {5881}, pages = {371-4} } @article{Ellis2004, author = {Ellis, C and Smith, A}, title = {Twenty quesions: the state of ion channel research in 2004}, journal = {Nature Reviews Drug Discovery}, volume = 3, year = 2004, pages = {237-278}, } @article{Engelman1986, author = {Engelman, DM and Steitz, TA and Goldman, A}, title = {Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins}, year = {1986}, volume = {15}, pages = {321-353}, journal = {Annu Rev Biophys Biophys Chem} } @article{Erhan1980, author = {Erhan, S and Marzolf, T and Cohen, L}, year = {1980}, title = {Amino-Acid Neighborhood Relationships in Proteins. Breakdown of Amino-Acid Sequences into Overlapping Doublets, Triplets and Quadruplets}, journal = {Int J Biomed Comput}, volume = {11}, issue = {1}, pages = {67-75} } @article{Fasman1990, author = {Fasman, GD and Gilbert, WA}, year = {1990}, title = {The Prediction of Transmembrane Protein Sequences and Their Conformation: An Evaluation}, journal = {Trends Biochem Sci}, volume = {15}, issue = {3}, pages = {89-92} } . . . Eur. J. Med. Chem. 18: @ARTICLE{Fauchere1983, AUTHOR = {Fauchere, JL and Pliska, V}, TITLE = {Hydrophobic parameters of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides}, JOURNAL = {Eur. J. Med. Chem}, YEAR = {1983}, volume = {18}, pages = {369–375}, month = {} } @article{Filipek2003, author = {Filipek, S and Stenkamp, RE and Teller, DC and Palczewski, K}, title = {G protein-coupled receptor rhodopsin: a prospectus}, journal = {Annu Rev Physiol}, year = {2003}, volume = 65, pages = {851-79} } @article{Filizola1998, author = {Filizola, M and Perez, JJ and Carteni-Farina, M}, title = {BUNDLE: a program for building the transmembrane domains of G-protein-coupled receptors}, journal = {J Comput Aided Mol Des}, year = {1998}, volume = {12}, issue = {2}, pages = {111-8} } @article{Fischer2003, author = {Fischer, P and Baudoux, G and Wouters, J}, year = {2003}, title = {Wavpred: A Wavelet-Based Algorithm for the Prediction of Transmembrane Proteins}, journal = {Comm. math. sci}, volume = {1}, issue = {1}, pages = {44 - 56} } @article{Frauenfelder2002, author = {Frauenfelder, H}, year = {2002}, title = {Proteins: Paradigms of Complexity}, journal = {Proc Natl Acad Sci U S A}, volume = {99 Suppl 1}, issue = {1}, pages = {2479-80} } @article{Frauenfelder1998, author = {Frauenfelder, H and McMahon, B}, year = {1998}, title = {Dynamics and Function of Proteins: The Search for General Concepts}, journal = {Proc Natl Acad Sci U S A}, volume = {95}, issue = {9}, pages = {4795-7} } @article{Frauenfelder2001, author = {Frauenfelder, H and McMahon, BH and Austin, RH and Chu, K and Groves, JT}, year = {2001}, title = {The Role of Structure, Energy Landscape, Dynamics, and Allostery in the Enzymatic Function of Myoglobin}, journal = {Proc Natl Acad Sci U S A}, volume = {98}, issue = {5}, pages = {2370-4} } @article{Frauenfelder2003, author = {Frauenfelder, H and McMahon, BH and Fenimore, PW}, year = {2003}, title = {Myoglobin: The Hydrogen Atom of Biology and a Paradigm of Complexity}, journal = {Proc Natl Acad Sci U S A}, volume = {100}, issue = {15}, pages = {8615-7} } @article{Frauenfelder1994, author = {Frauenfelder, H and Wolynes, PG}, year = {1994}, title = {Proteins: Where the Physics of Simplicity and Complexity Meet}, journal = {Physics Today}, volume = {47}, issue = {15}, pages = {58-64} } @article{Frishman1996, author = {Frishman, D and Argos, P}, year = {1996}, title = {Incorporation of Non-Local Interactions in Protein Secondary Structure Prediction from the Amino Acid Sequence}, journal = {Protein Eng}, volume = {9}, issue = {2}, pages = {133-42} } @article{Frishman1997, author = {Frishman, D and Argos, P}, year = {1997}, title = {Seventy-Five Percent Accuracy in Protein Secondary Structure Prediction}, journal = {Proteins}, volume = {27}, issue = {3}, pages = {329-35} } @article{Ganapathiraju2004IEEE, author = {Ganapathiraju, M and Klein-Seetharaman, J and Balakrishnan, N and Reddy, R}, year = {2004}, title = {Characterization of Protein Secondary Structure Using Latent Semantic Analysis}, journal = {IEEE Signal Processing magazine}, volume = {21}, issue = {3}, pages = {78-87} } @conference{Ganapathiraju2002RECOMB, author = {Ganapathiraju, M and Klein-Seetharaman, J and Rosenfeld, R and Carbonell, J and Reddy, R}, year = {2002}, title = {Rare and Frequent Amino Acid N-Grams in Whole-Genome Protein Sequences}, booktitle = {RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology}, location = {}, pages = {} } @conference{Ganapathiraju2004SCI, author = {Ganapathiraju, M and Weisser, D and Klein-Seetharaman, J}, year = {2004}, title = {Yule Value Tables from Protein Datasets}, booktitle = {Eighth Multiconfernece on Systemics, Cybernetics and Informatics} } @conference{Ganapathiraju2002HLT, author = {Ganapathiraju, M and Weisser, D and Rosenfeld, R and Carbonell, J and Reddy, R and Klein-Seetharaman, J}, year = {2002}, title = {Comparative N-Gram Analysis of Whole-Genome Sequences}, booktitle = {HLT2002: Human Language Technologies Conference}, location = {}, pages = {} } @conference{Gao2000, author = {Gao, J and Lee, K-F}, year = {2000}, title = {Distribution-Based Pruning of Backoff Language Models}, booktitle = {ACL00: The 38th Annual Meeting of the Association for Computational Linguistics}, location = {}, pages = {78-87} } @article{Gerstein1997, author = {Gerstein, M}, year = {1997}, title = {A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaeal Genomes in Terms of Protein Structure}, journal = {J Mol Biol}, volume = {274}, issue = {4}, pages = {562-76} } @article{Gerstein1998, author = {Gerstein, M}, year = {1998}, title = {Patterns of Protein-Fold Usage in Eight Microbial Genomes: A Comprehensive Structural Census}, journal = {Proteins}, volume = {33}, issue = {4}, pages = {518-34.} } @article{Gerstein1998, author = {Gerstein, M and Hegyi, H}, year = {1998}, title = {Comparing Genomes in Terms of Protein Structure: Surveys of a Finite Parts List}, journal = {FEMS Microbiol Rev}, volume = {22}, issue = {4}, pages = {277-304} } @article{Gerstein2000, author = {Gerstein, M, Lin, J and Hegyi, H}, year = {2000}, title = {Protein Folds in the Worm Genome}, journal = {Pac Symp Biocomput}, volume = {22}, issue = {4}, pages = {30-41} } @article{Goodfellow1991, author = {Goodfellow, PN and Sefton, L}, title = {Human genetics. Language of the genome} year = {1991} journal = {Nature}, volume = {353}, issue = {6340}, pages = {117-8} } @book{Gibas2001, author = {Gibas, C and Jambeck, P}, year = {2001}, title = {Developing Bioinformatics Computer Skills}, publisher = {O'Reilly \& Associates} } @article{Gibrat1987, author = {Gibrat, JF and Garnier, J and Robson, B}, year = {1987}, title = {Further Developments of Protein Secondary Structure Prediction Using Information Theory. New Parameters and Consideration of Residue Pairs}, journal = {J Mol Biol}, volume = {198}, issue = {3}, pages = {425-43} } @article{Giuliani2002, author = {Giuliani, A and Benigni, R and Zbilut, JP and Webber, CL Jr. and Sirabella, P and Colosimo, A}, year = {2002}, title = {Nonlinear Signal Analysis Methods in the Elucidation of Protein Sequence-Structure Relationships}, journal = {Chem Rev}, volume = {102}, issue = {5}, pages = {1471-92} } @conference{Gong2001, author = {Gong, Y and Liu, X}, year = {2001}, title = {Generic Text Summarization Using Relevance Measure and Latent Semantic Analysis}, booktitle = {ACM SIGIR'01}, location = {}, pages = {1471-92} } @article{Gottschalk2002, author = {Gottschalk, KE and Kessler, H}, title = {The structures of integrins and integrin-ligand complexes: implications for drug design and signal transduction}, year = {2002}, journal = {Angew Chem Int Ed Engl}, volume = {41}, issue = {20}, pages = {3767-74} } @article{Graps1995, author = {Graps, A}, year = {1995}, title = {An Introduction to Wavelets}, journal = {Computational Science and Engineering, IEEE [see also Computing in Science \& Engineering]}, volume = {2}, issue = {2}, pages = {50-61} } @article{Gromiha2004, author = {Gromiha, MM and Ahmad, S and Suwa, M}, year = {2004}, title = {Neural Network-Based Prediction of Transmembrane Beta-Strand Segments in Outer Membrane Proteins}, journal = {J Comput Chem}, volume = {25}, issue = {5}, pages = {762-7} } @article{Gromiha1993, author = {Gromiha, MM and Ponnuswamy, PK}, year = {1993}, title = {Prediction of Transmembrane Beta-Strands from Hydrophobic Characteristics of Proteins}, journal = {Int J Pept Protein Res}, volume = {42}, issue = {5}, pages = {420-31} } @conference{Gupta2001, author = {Gupta, M and Gilbert, A}, year = {2001}, title = {Robust Speech Recognition Using Wavelet Coefficient Features}, booktitle = {ASRU01: IEEE Workshop on Automatic Speech Recognition and Understanding}, location = {}, pages = {420-31} } @article{Head1987, author = {Head, T}, year = {1987}, title = {Formal Language Theory and DNA: An Analysis of the Generative Capacity of Specific Recombinant Behaviors} journal = {MBull. math. Biol}, volume = {49}, issue = {6}, pages = {737-759} } @conference{Hofman1999, author = {Hofman, T}, year = {1999}, title = {Probabilistic Latent Semantic Analysis}, booktitle = {SIGIR'99}, location = {}, pages = {420-31} } @conference{Huang1996, author = {Huang, CC and Couch, GS and Pettersen, EF and Ferrin, TE}, year = {1996}, title = {Chimera): An Extensible Molecular Modeling Application Constructed Using Standard Components (Http://Www.Cgl.Ucsf.Edu/Chimera)}, booktitle = {PSB1996: Pacific Symposium on Biocomputing}, location = {}, pages = {420-31} } @article{Hucka2002, author = {Hucka, M and Finney, A and Sauro, HM and Bolouri, H and Doyle, J and Kitano, H}, year = {2002}, title = {The Erato Systems Biology Workbench: Enabling Interaction and Exchange between Software Tools for Computational Biology}, journal = {Pac Symp Biocomput}, volume = {42}, issue = {5}, pages = {450-61} } @article{Ikeda2002, author = {Ikeda, M and Arai, M and Lao, DM and Shimizu, T}, year = {2002}, title = {Transmembrane Topology Prediction Methods: A Re-Assessment and Improvement by a Consensus Method Using a Dataset of Experimentally-Characterized Transmembrane Topologies}, journal = {In Silico Biol}, volume = {2}, issue = {1}, pages = {19-33} } @article{Israeloff1996, author = {Israeloff, NE and Kagalenko, M and Chan, K}, year = {1996}, title = {Can Zipf Distinguish Language from Noise in Noncoding DNA?}, journal = {Physical Review Letters}, volume = {76}, issue = {11}, pages = {1976} } @article{Jacoboni2001, author = {Jacoboni, I and Martelli, PL and Fariselli, P and De Pinto, V and Casadio, R}, year = {2001}, title = {Prediction of the Transmembrane Regions of Beta-Barrel Membrane Proteins with a Neural Network-Based Predictor}, journal = {Protein Sci}, volume = {10}, issue = {4}, pages = {779-87} } @book{Jain1988, author = {Jain, AK}, year = {1988}, title = {Fundamentals of Digital Image Processing}, publisher = {Prentice Hall} } @article{Jayasinghe2001, author = {Jayasinghe, S and Hristova, K and White, SH}, year = {2001}, title = {Energetics, Stability, and Prediction of Transmembrane Helices}, journal = {J Mol Biol}, volume = {312}, issue = {5}, pages = {927-34} } @article{kabsch1983, author = {Kabsch, W and Sander, C}, year = {1983}, title = {Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features}, journal = {Biopolymers}, volume = {22}, issue = {12}, pages = {2577-637} } @article{Kall2004, author = {Kall, L and Krogh, A and Sonnhammer, EL}, year = {2004}, title = {A Combined Transmembrane Topology and Signal Peptide Prediction Method}, journal = {J Mol Biol}, volume = {338}, issue = {5}, pages = {1027-36} } @misc{Karchin2002, author = {Karchin, R and Karplus, K and Haussler, D}, year = {2002}, title = {Classifying G-Protein Coupled Receptors with Support Vector Machines}, } @article{Karlin1990, author = {Karlin, S, Blaisdell, BE and Brendel, V}, year = {1990}, title = {Identification of Significant Sequence Patterns in Proteins}, journal = {Methods Enzymol}, volume = {183}, issue = {11}, pages = {388-402} } @article{Karlin1992, author = {Karlin, S and Blaisdell, BE and Bucher, P}, year = {1992}, title = {Quantile Distributions of Amino Acid Usage in Protein Classes}, journal = {Protein Eng}, volume = {5}, issue = {8}, pages = {729-38} } @article{Karlin1991, author = {Karlin, S and Bucher, P and Brendel, V and Altschul, SF}, year = {1991}, title = {Statistical Methods and Insights for Protein and DNA Sequences}, journal = {Annu Rev Biophys Biophys Chem}, volume = {20}, issue = {8}, pages = {175-203} } @article{Karlin1994, author = {Karlin, S and Cardon, LR}, year = {1994}, title = {Computational DNA Sequence Analysis}, journal = {Annu Rev Microbiol}, volume = {48}, issue = {4}, pages = {619-54} } @article{Karlin1995, author = {Karlin, S and Burge, C}, year = {1995}, title = {Dinucleotide Relative Abundance Extremes: A Genomic Signature}, journal = {Trends Genet}, volume = {11}, issue = {7}, pages = {283-90} } @article{Karlin1996, author = {Karlin, S and Burge, C}, year = {1996}, title = {Trinucleotide Repeats and Long Homopeptides in Genes and Proteins Associated with Nervous System Disease and Development}, journal = {Proc Natl Acad Sci U S A}, volume = {93}, issue = {4}, pages = {1560-5} } @conference{Kasai2001, author = {Kasai, T and Lee, G and Arimura, H and Arikawa, S and Park, K}, year = {2001}, title = {Linear-Time Longest-Common-Prefix Computation in Suffix Arrays and Its Applications}, booktitle = {Annual Symposium on Combinatorial Pattern Matching CPM-2001}, location = {}, pages = {1560-5} } @article{Kay1998, author = {Kay, LE}, title = {A book of life? How the genome became an information system and DNA a language}, year = {1998}, journal = {Perspect Biol Med}, volume = {41}, issue = {4}, pages = {504-28} } @article{Kihara1998, author = {Kihara, D and Shimizu, T and Kanehisa, M}, year = {1998}, title = {Prediction of Membrane Proteins Based on Classification of Transmembrane Segments}, journal = {Protein Eng}, volume = {11}, issue = {11}, pages = {961-70} } @conference{Klein-Seetharaman2002, author = {Klein-Seetharaman, J and Ganapathiraju, M and Rosenfeld, R and Carbonell, J and Reddy, R}, year = {2002}, title = {Rare and Frequent Amino Acid N-Grams in Whole-Genome Protein Sequences}, booktitle = {RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology}, location = {}, pages = {961-70} } @article{Klein-Seetharaman2002, author = {Klein-Seetharaman, J and Oikawa, M and Grimshaw, SB and Wirmer, J and Duchardt, E and Ueda, T and Imoto, T and Smith, LJ and Dobson, CM and Schwalbe, H}, year = {2002}, title = {Long-Range Interactions within a Nonnative Protein}, journal = {Science}, volume = {295}, issue = {5560}, pages = {1719-22} } @article{Klein-Seetharaman2003, author = {Klein-Seetharaman, J}, year = {2002}, title = {Dynamics in Rhodopsin}, journal = {ChemBioChem}, volume = {3}, pages = {981-986} } @book{Konopka1994, author = {Konopka, AK}, title = {Sequences and Codes: Fundamentals of Biomolecular Cryptology} editor = {D. W. Smith}, publisher = {Academic Press}, year= {1994} } @article{Konopka1995, author = {Konopka, AK and Martindale, C}, year = {1995}, title = {Noncoding DNA, Zipf's Law, and Language}, journal = {Science}, volume = {268}, issue = {5212}, pages = {789.} } @article{Kraljevic2004, author = {Kraljevic, S and Stambrook, PJ and Pavelic, K}, title = {Accelerating drug discovery}, year = {2004}, journal = {EMBO reports}, volume = 5, number = 9, pages = {837-842} } @article{Krogh2001, author={Krogh, A and Larsson, B and von Heijne, G and Sonnhammer, EL}, title = {Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes}, journal = {J Mol Biol}, year = {2001}, volume = {305}, issue = {3}, pages = {567-80} } @ARTICLE{Kurgan2005, AUTHOR = {Kurgan, L and Homaeian, L}, TITLE = {Prediction of Secondary Protein Structure Content from Primary Sequence Alone – A Feature Selection Based Approach}, JOURNAL = {Lecture Notes in Computer Science}, YEAR = {2005}, volume = {3587}, pages = {334-345} } @misc{Kuznetsov2003, author = {Kuznetsov, IB and Rackovsky, S}, year = {2003}, title = {On the Properties and Sequence Context of Structurally Ambivalent Fragments in Proteins} , } @article{Kyte1982, author = {Kyte, J and Doolittle, RF}, year = {1982}, title = {A simple method for displaying the hydropathic character of a protien}, journal = {J Mol Biol}, volume = {157}, issue = {1}, pages = {105-132} } @article{Lacroix1998, author = {Lacroix, E and Viguera, AR and Serrano, L}, year = {1998}, title = {Elucidating the Folding Problem of Alpha-Helices: Local Motifs, Long-Range Electrostatics, Ionic-Strength Dependence and Prediction of Nmr Parameters}, journal = {J Mol Biol}, volume = {284}, issue = {1}, pages = {173-91} } @article{Lander2001, author = {Lander, ES and Linton, LM and Birren, B and Nusbaum, C and Zody, MC and Baldwin, J and Devon, K and Dewar, K and Doyle, M and FitzHugh, W and Funke, R and Gage, D and Harris, K and Heaford, A and Howland, J and Kann, L and Lehoczky, J and LeVine, R and McEwan, P and McKernan, K and Meldrim, J and Mesirov, JP and Miranda, C and Morris, W and Naylor, J and Raymond, C and Rosetti, M and Santos, R and Sheridan, A and Sougnez, C and Stange-Thomann, N and Stojanovic, N and Subramanian, A and Wyman, D and Rogers, J and Sulston, J and Ainscough, R and Beck, S and Bentley, D and Burton, J and Clee, C and Carter, N and Coulson, A and Deadman, R and Deloukas, P and Dunham, A and Dunham, I and Durbin, R and French, L and Grafham, D and Gregory, S and Hubbard, T and Humphray, S and Hunt, A and Jones, M and Lloyd, C and McMurray, A and Matthews, L and Mercer, S and Milne, S and Mullikin, JC and Mungall, A and Plumb, R and Ross, M and Shownkeen, R and Sims, S and Waterston, RH and Wilson, RK and Hillier, LW and McPherson, JD and Marra, MA and Mardis, ER and Fulton, LA and Chinwalla, AT and Pepin, KH and Gish, WR and Chissoe, SL and Wendl, MC and Delehaunty, KD and Miner, TL and Delehaunty, A and Kramer, JB and Cook, LL and Fulton, RS and Johnson, DL and Minx, PJ and Clifton, SW and Hawkins, T and Branscomb, E and Predki, P and Richardson, P and Wenning, S and Slezak, T and Doggett, N and Cheng, JF and Olsen, A and Lucas, S and Elkin, C and Uberbacher, E and Frazier, M and Gibbs, RA and Muzny, DM and Scherer, SE and Bouck, JB and Sodergren, EJ and Worley, KC and Rives, CM and Gorrell, JH and Metzker, ML and Naylor, SL and Kucherlapati, RS and Nelson, DL and Weinstock, GM and Sakaki, Y and Fujiyama, A and Hattori, M and Yada, T and Toyoda, A and Itoh, T and Kawagoe, C and Watanabe, H and Totoki, Y and Taylor, T and Weissenbach, J and Heilig, R and Saurin, W and Artiguenave, F and Brottier, P and Bruls, T and Pelletier, E and Robert, C and Wincker, P and Smith, DR and Doucette-Stamm, L and Rubenfield, M and Weinstock, K and Lee, HM and Dubois, J and Rosenthal, A and Platzer, M and Nyakatura, G and Taudien, S and Rump, A and Yang, H and Yu, J and Wang, J and Huang, G and Gu, J and Hood, L and Rowen, L and Madan, A and Qin, S and Davis, RW and Federspiel, NA and Abola, AP and Proctor, MJ and Myers, RM and Schmutz, J and Dickson, M and Grimwood, J and Cox, DR and Olson, MV and Kaul, R and Shimizu, N and Kawasaki, K and Minoshima, S and Evans, GA and Athanasiou, M and Schultz, R and Roe, BA and Chen, F and Pan, H and Ramser, J and Lehrach, H and Reinhardt, R and McCombie, WR and de la Bastide, M and Dedhia, N and Blocker, H and Hornischer, K and Nordsiek, G and Agarwala, R and Aravind, L and Bailey, JA and Bateman, A and Batzoglou, S and Birney, E and Bork, P and Brown, DG and Burge, CB and Cerutti, L and Chen, HC and Church, D and Clamp, M and Copley, RR and Doerks, T and Eddy, SR and Eichler, EE and Furey, TS and Galagan, J and Gilbert, JG and Harmon, C and Hayashizaki, Y and Haussler, D and Hermjakob, H and Hokamp, K and Jang, W and Johnson, LS and Jones, TA and Kasif, S and Kaspryzk, A and Kennedy, S and Kent, WJ and Kitts, P and Koonin, EV and Korf, I and Kulp, D and Lancet, D and Lowe, TM and McLysaght, A and Mikkelsen, T and Moran, JV and Mulder, N and Pollara, VJ and Ponting, CP and Schuler, G and Schultz, J and Slater, G and Smit, AF and Stupka, E and Szustakowski, J and Thierry-Mieg, D and Thierry-Mieg, J and Wagner, L and Wallis, J and Wheeler, R and Williams, A and Wolf, YI and Wolfe, KH and Yang, SP and Yeh, RF and Collins, F and Guyer, MS and Peterson, J and Felsenfeld, A and Wetterstrand, KA and Patrinos, A and Morgan, MJ and Szustakowki, J}, year = {2001}, title = {Initial Sequencing and Analysis of the Human Genome}, journal = {Nature}, volume = {409}, issue = {6822}, pages = {860-921} } @article{Landauer1998, author = {Landauer, T and Foltx, P and Laham, D}, year = {1998}, title = {Introduction to Latent Semantic Analysis}, journal = {Discourse Processes}, volume = {25}, issue = {1}, pages = {259-284} } @conference{Landauer1997, author = {Landauer, T and Laham, D and Rehder, B and Schreiner, M}, year = {1997}, title = {19th Annual Meeting of the Cognitive Science Society}, booktitle = {RECOMB'02: The Sixth Annual International Conference on Research in Computational Molecular Biology}, location = {}, pages = {259-284} } @article{Lao2002, author = {Lao, DM and Arai, M and Ikeda, M and Shimizu, T}, year = {2002}, title = {The Presence of Signal Peptide Significantly Affects Transmembrane Topology Prediction}, journal = {Bioinformatics}, volume = {18}, issue = {12}, pages = {1562-6} } @article{Lao2002, author = {Lao, DM and Okuno, T and Shimizu, T}, year = {2002}, title = {Evaluating Transmembrane Topology Prediction Methods for the Effect of Signal Peptide in Topology Prediction}, journal = {In Silico Biol}, volume = {2}, issue = {4}, pages = {485-94} } @article{Leung2001, author = {Leung, S, Mellish, C and Robertson, D}, year = {2001}, title = {Basic Gene Grammars and DNA-Chartparser for Language Processing of Escherichia Coli Promoter DNA Sequences}, journal = {Bioinformatics}, volume = {17}, issue = {3}, pages = {226-36} } @INPROCEEDINGS{Li2004, AUTHOR = {Li, M-H and Wang, X-L and Lin, L and Guan, Y}, TITLE = {Protein secondary structure pattern discovery and its application in secondary structure prediction}, BOOKTITLE = {Procecdmgs of the Third International Conference on Machine Learning and Cybemetics}, YEAR = {2004}, pages = {1435-40} } @article{Li1999, author = {Li, W}, year = {1999}, title = {Statistical Properties of Open Reading Frames in Complete Genome Sequences}, journal = {Comput Chem}, volume = {23}, issue = {3-4}, pages = {283-301.} } @article{Liakopoulos2001, author = {Liakopoulos, TD and Pasquier, C and Hamodrakas, SJ}, year = {2001}, title = {A Novel Tool for the Prediction of Transmembrane Protein Topology Based on a Statistical Analysis of the Swissprot Database: The Orientm Algorithm}, journal = {Protein Eng}, volume = {14}, issue = {6}, pages = {387-90} } @article{Lio2000, author = {Lio, P and Vannucci, M}, year = {2000}, title = {Wavelet Change-Point Prediction of Transmembrane Proteins}, journal = {Bioinformatics}, volume = {16}, issue = {4}, pages = {376-82} } @article{Liu1999, author = {Liu, W and Chou, KC}, year = {1999}, title = {Prediction of Protein Secondary Structure Content}, journal = {Protein Eng}, volume = {12}, issue = {12}, pages = {1041-50} } @article{Liu2004B, author = {Liu, Y and Carbonell, J and Klein-Seetharaman, J and Gopalakrishnan, V}, year = {2004}, title = {Comparison of Probabilistic Combination Methods for Protein Secondary Structure Prediction}, journal = {Bioinformatics}, volume = {12}, issue = {12}, pages = {1041-50} } @article{LoConte2002, author = {Lo Conte L and Brenner, SE and Hubbard, TJ and Chothia, C and Murzin, AG}, year = {2002}, title = {Scop Database in 2002: Refinements Accommodate Structural Genomics}, journal = {Nucleic Acids Res}, volume = {30}, issue = {1}, pages = {264-7} } @article{Lomize2006, author = {Lomize, MA and Lomize, AL and Pogozheva, ID and Mosberg, HI}, year = {2006}, title = {OPM: Orientations of Proteins in Membranes database}, journal = {Bioinformatics}, volume = {22}, page = {623-625} } @article{Lundin2003, author = {Lundin, C and Schultz, N and Arnaudeau, C and Mohindra, A and Hansen, L and Helleday, T}, year = {2003}, title = {Rad51 Is Involved in Repair of Damage Associated with DNA Replication in Mammalian Cells}, journal = {Journal of Molecular Biology}, volume = {328}, issue = {3}, pages = {521-535} } @article{MacKenzie1998, author = {MacKenzie, KR and Engelman, DM}, year = {1998}, title = {Structure-Based Prediction of the Stability of Transmembrane Helix-Helix Interactions: The Sequence Dependence of Glycophorin a Dimerization}, journal = {Proc Natl Acad Sci U S A}, volume = {95}, issue = {7}, pages = {3583-90} } @article{Mahadevan1999, author = {Mahadevan, D and Saldanha, JW}, title = {The extracellular regions of PSMA and the transferrin receptor contain an aminopeptidase domain: implications for drug design}, year = {1999}, journal = {Protein Sci}, volume = {8}, issue = {11}, pages = {2546-9} } @article{Manber1993, author = {Manber, U and Myers, G}, year = {1993}, title = {Suffix Arrays: A New Method for on-Line String Searches}, journal = {SIAM Journal on Computing}, volume = {22}, issue = {5}, pages = {935-948} } @article{Mandel-Gutfreund2002, author = {Mandel-Gutfreund, Y and Gregoret, LM}, year = {2002}, title = {On the Significance of Alternating Patterns of Polar and Non-Polar Residues in Beta-Strands}, journal = {J Mol Biol}, volume = {323}, issue = {3}, pages = {453-61} } @book{Manning1999, AUTHOR = {Manning, C and Schutze, H}, TITLE = {Foundations of Statistical Natural Language Processing}, PUBLISHER = {MIT Press}, YEAR = {1999}, address = {Cambridge, MA, USA}, month = {May}, } @article{Mantegna1994, author = {Mantegna, RN and Buldyrev, SV and Goldberger, AL and Havlin, S and Peng, CK and Simons, M and Stanley, HE}, year = {1994}, title = {Linguistic Features of Noncoding DNA Sequences}, journal = {Phys Rev Lett}, volume = {73}, issue = {23}, pages = {3169-72} } @ARTICLE{Mantegna1995, author = {Mantegna, RN and Buldyrev, SV and Goldberger, AL and Havlin, S and Peng, CK and Simons, M and Stanley, HE}, TITLE = {Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics}, JOURNAL = {Phys. Rev}, YEAR = {1995}, volume = {E 52}, number = {3}, pages = {2939 - 2950}, month = {September} } @article{Miller1958, author = {Miller, GA and Newman, EB}, year = {1958}, title = {Tests of a Statistical Explanation of the Rank-Frequency Relation for Words in Written English}, journal = {American Journal of Psychology}, volume = {71}, issue = {23}, pages = {209-218} } @article{Mishra2003, author = {Mishra, B and Daruwala, RS and Zhou, Y, et al}, title = {A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes}, year = {2003}, volume = {7}, pages = {253-268}, issue = {3}, journal = {Omics} } @article{Mugilan2000, author = {Mugilan, SA and Veluraja, K}, year = {2000}, title = {Generation of Deviation Parameters for Amino Acid Singlets, Doublets and Triplets from Three-Dimentional Structures of Proteins and Its Implications for Secondary Structure Prediction from Amino Acid Sequences}, journal = {J Biosci}, volume = {25}, issue = {1}, pages = {81-91} } @article{Muller-Hill1999, author = {Muller-Hill, B}, title = {Towards a linguistics of DNA and protein}, year = {1999}, journal = {Hist Philos Life Sci}, volume = {21}, issue = {1}, pages = {53-63} } @article{Muraoka2003, author = {Muraoka, S and Okumura, R and Ogawa, N and Nonaka, T and Miyashita, K and Senda, T}, year = {2003}, title = {Crystal Structure of a Full-Length Lysr-Type Transcriptional Regulator, Cbnr: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend}, journal = {Journal of Molecular Biology}, volume = {328}, issue = {3}, pages = {555-566} } @article{Murzin1995, author = {Murzin, AG and Brenner, SE and Hubbard, T and Chothia, C}, year = {1995}, title = {Scop: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures}, journal = {J Mol Biol}, volume = {247}, issue = {4}, pages = {536-40} } @article{Natt2004, author = {Natt, NK and Kaur, H and Raghava, GP}, year = {2004}, title = {Prediction of Transmembrane Regions of Beta-Barrel Proteins Using Ann- and Svm-Based Methods}, journal = {Proteins}, volume = {56}, issue = {1}, pages = {11-8} } @ARTICLE{Donovan2001, AUTHOR = {O'Donovan, C and Apweiler, R and Bairoch, A}, TITLE = {The human proteomics initiative}, JOURNAL = {Trends Biotechnol}, YEAR = {2001}, volume = {19}, number = {5}, pages = {178-81} } @article{Ott2002, author = {Ott, CM and Lingappa, VR}, title = {Integral membrane protein biosynthesis: why topology is hard to predict}, journal = {J Cell Sci}, year = {2002}, volume = {115}, pages = {2003-9} } @article{Pashou2004, author = {Pashou, EE and Litou, ZI and Liakopoulos, TD and Hamodrakas, SJ}, year = {2004}, title = {Wavetm: Wavelet-Based Transmembrane Segment Prediction}, journal = {In Silico Biol}, volume = {4}, issue = {2}, pages = {0012} } @article{Pasquier1998, author = {Pasquier, CM and Promponas, VV and Varvayannis, NJ and Hamodrakas, SJ}, year = {1998}, title = {A Web Server to Locate Periodicities in a Sequence}, journal = {Bioinformatics}, volume = {14}, issue = {8}, pages = {749-50} } @article{pdbase1998, author = {PDBase}, year = {1998}, title = {Http://Www.Scsb.Utmb.Edu/Comp\_Biol.Html/Venkat/Prop.Html}, journal = {Bioinformatics}, volume = {14}, issue = {8}, pages = {749-50} } @article{Pietrokovski1992, year = {1992}, author = {Pietrokovski S and Trifonov EN}, title = {Imported sequences in the mitochondrial yeast genome identified by nucleotide linguistics}, journal = {Gene}, volume = {122}, issue = {1}, pages = {129-137} } @article{Persson1994, author = {Persson, B and Argos, P}, year = {1994}, title = {Prediction of Transmembrane Segments in Proteins Utilising Multiple Sequence Alignments}, journal = {J Mol Biol}, volume = {237}, issue = {2}, pages = {182-92} } @article{Petersen2000, author = {Petersen, TN and Lundegaard, C and Nielsen, M and Bohr, H and Bohr, J and Brunak, S and Gippert, GP and Lund, O}, year = {2000}, title = {Prediction of Protein Secondary Structure at 80% Accuracy}, journal = {Proteins}, volume = {41}, issue = {1}, pages = {17-20} } @article{Pilpel1999, author = {Pilpel, Y and Ben-Tal, N and Lancet, D}, year = {1999}, title = {Kprot: A Knowledge-Based Scale for the Propensity of Residue Orientation in Transmembrane Segments. Application to Membrane Protein Structure Prediction}, journal = {J Mol Biol}, volume = {294}, issue = {4}, pages = {921-35} } @article{Pizza2000, author = {Pizza, M and Scarlato, V and Masignani, V and Giuliani, MM and Arico, B and Comanducci, M and Jennings, GT and Baldi, L and Bartolini, E and Capecchi, B and Galeotti, CL and Luzzi, E and Manetti, R and Marchetti, E and Mora, M and Nuti, S and Ratti, G and Santini, L and Savino, S and Scarselli, M and Storni, E and Zuo, P and Broeker, M and Hundt, E and Knapp, B and Blair, E and Mason, T and Tettelin, H and Hood, DW and Jeffries, AC and Saunders, NJ and Granoff, DM and Venter, JC and Moxon, ER and Grandi, G and Rappuoli, R}, year = {2000}, title = {Identification of Vaccine Candidates against Serogroup B Meningococcus by Whole-Genome Sequencing}, journal = {Science}, volume = {287}, issue = {5459}, pages = {1816-20} } @article{Pollastri2002, author = {Pollastri, G and Przybylski, D and Rost, B and Baldi, P}, year = {2002}, title = {Improving the Prediction of Protein Secondary Structure in Three and Eight Classes Using Recurrent Neural Networks and Profiles}, journal = {Proteins}, volume = {47}, issue = {2}, pages = {228-35} } @article{Ponnuswamy1993, author = {Ponnuswamy, PK and Gromiha, MM}, year = {1993}, title = {Prediction of Transmembrane Helices from Hydrophobic Characteristics of Proteins}, journal = {Int J Pept Protein Res}, volume = {42}, issue = {4}, pages = {326-41} } @book{Proakis1992, author = {Proakis, JG and Manolakis, D}, year = {1992}, title = {Digital Signal Processing: Principles, Algorithms and Applications}, publisher = {Macmillan USA} } @article{Promponas1999, author = {Promponas, VJ and Palaios, GA and Pasquier, CM and Hamodrakas, JS and Hamodrakas, SJ}, year = {1999}, title = {Coprethi: A Web Tool Which Combines Transmembrane Protein Segment Prediction Methods}, journal = {In Silico Biol}, volume = {1}, issue = {3}, pages = {159-62} } @article{protscale1999, author = {ProtScale}, year = {1999}, title = {Www.Expasy.Ch/Cgi-Bin/Protscale.Pl}, journal = {In Silico Biol}, volume = {1}, issue = {3}, pages = {159-62} } @article{Qiu2004, author = {Qiu, J and Liang, R and Zou, X and Mo, J}, year = {2004}, title = {Prediction of Transmembrane Proteins Based on the Continuous Wavelet Transform}, journal = {J Chem Inf Comput Sci}, volume = {44}, issue = {2}, pages = {741-7} } @book{Rabiner1993, author = {Rabiner, L and Juang, B-H}, year = {1993}, title = {Fundamentals of Speech Recognition}, publisher = {Pearson Education POD} } @article{Richardson1988, author = {Richardson, JS and Richardson, DC}, year = {1988}, title = {Amino Acid Preferences for Specific Locations at the Ends of Alpha Helices}, journal = {Science}, volume = {240}, issue = {4859}, pages = {1648-52} } @article{Rivals1996, author = {Rivals, E and Dauchet, M and Delahaye, JP and Delgrange, O}, year = {1996}, title = {Compression and Genetic Sequence Analysis}, journal = {Biochimie}, volume = {78}, issue = {5}, pages = {315-22} } @article{Rivas2000, author = {Rivas, E and Eddy, SR}, year = {2000}, title = {The Language of Rna: A Formal Grammar That Includes Pseudoknots}, journal = {Bioinformatics}, volume = {16}, issue = {4}, pages = {334-40} } @article{Romero2001, author = {Romero, P, Obradovic, Z, Li, X, Garner, EC, Brown, CJ and Dunker, AK}, year = {2001}, title = {Sequence Complexity of Disordered Protein}, journal = {Proteins}, volume = {42}, issue = {1}, pages = {38-48.} } @article{Rost2001, author = {Rost, B}, year = {2001}, title = {Review: Protein Secondary Structure Prediction Continues to Rise}, journal = {J Struct Biol}, volume = {134}, issue = {2-3}, pages = {204-18} } @article{Rost1996, author = {Rost, B and Fariselli, P and Casadio, R}, year = {1996}, title = {Topology Prediction for Helical Transmembrane Proteins at 86% Accuracy}, journal = {Protein Sci}, volume = {5}, issue = {8}, pages = {1704-18} } @article{Rost1993, author = {Rost, B and Sander, C}, year = {1993}, title = {Improved Prediction of Protein Secondary Structure by Use of Sequence Profiles and Neural Networks}, journal = {Proc Natl Acad Sci U S A}, volume = {90}, issue = {16}, pages = {7558-62} } @ARTICLE{Ruan2005, AUTHOR = {Ruan, J and Wang, K and Yang, J and Kurgan, LA and Cios, K}, TITLE = {Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences}, JOURNAL = {Artificial Intelligence in Medicine}, YEAR = {2005}, volume = {35}, pages = {19-35} } @misc{Sadakane2001, author = {Sadakane, K and Shibuya, T}, year = {2001}, title = {Indexing Huge Genome Sequences for Solving Various Problems} , } @article{Schmidler2000, author = {Schmidler, SC and Liu, JS and Brutlag, DL}, year = {2000}, title = {Bayesian Segmentation of Protein Secondary Structure}, journal = {J Comput Biol}, volume = {7}, issue = {1-2}, pages = {233-48} } @article{Schneider2000, author = {Schneider, TD}, year = {2000}, title = {Evolution of Biological Information}, journal = {Nucleic Acids Res}, volume = {28}, issue = {14}, pages = {2794-9} } @article{Searls1988, author = {Searls, DB}, year = {1988}, title = {Representing Genetic Information with Formal Grammars}, journal = {In: Proceedings of the 7th national conference on artificial intelligence}, volume = {42}, issue = {1}, pages = {386-391} } @misc{Searls1989, author = {Searls, DB}, year = {1989}, title = {Investigating the Linguistics of DNA with Definite Clause Grammars}, } @article{Searls1989b, author = {Searls, DB}, year = {1989}, title = {Signal Processing with Logic Grammars}, journal = {Intelligent Systems Rev.}, volume = {1}, issue = {4}, pages = {67-88} } @misc{Searls1990, author = {Searls, DB and Liebowitz, S}, year = {1990}, title = {Logic Grammars as a Vehicle for Syntactic Pattern Recognition}, } @misc{Searls1991, author = {Searls, DB and Noordewier, MO}, year = {1991}, title = {Pattern-Matching Search of DNA Sequences Using Logic Grammars}, } @article{Searls2000, author = {Searls, DB}, year = {2000}, title = {Bioinformatics Tools for Whole Genomes}, journal = {Annu Rev Genomics Hum Genet}, volume = {1}, issue = {14}, pages = {251-79} } @article{Searls2001, author = {Searls, DB}, year = {2001}, title = {Reading the Book of Life}, journal = {Bioinformatics}, volume = {17}, issue = {7}, pages = {579-80} } @article{Searls2002, author = {Searls, DB}, year = {2002}, title = {The Language of Genes}, journal = {Nature}, volume = {420}, issue = {6912}, pages = {211-7} } @article{Seidenberg2002, author = {Seidenberg, MS and MacDonald, MC and Saffran, JR}, year = {2002}, title = {Neuroscience. Does Grammar Start Where Statistics Stop?}, journal = {Science}, volume = {298}, issue = {5593}, pages = {553-4} } @article{Selbig1999, author = {Selbig, J and Mevissen, T and Lengauer, T}, year = {1999}, title = {Decision Tree-Based Formation of Consensus Protein Secondary Structure Prediction}, journal = {Bioinformatics}, volume = {15}, issue = {12}, pages = {1039-46} } @article{Serra-Hartmann2000, author = {Serra-Hartmann, X, Rebordosa, X, Pinol, J, Querol, E and Marti-Renom, MA}, year = {2000}, title = {Asap: Analysis of Peptide Composition}, journal = {Bioinformatics}, volume = {16}, issue = {12}, pages = {1153-4.} } @article{Shih2003, author = {Shih, ES and Hwang, MJ}, year = {2003}, title = {Protein Structure Comparison by Probability-Based Matching of Secondary Structure Elements}, journal = {Bioinformatics}, volume = {19}, issue = {6}, pages = {735-41} } @misc{Simons1999, author = {Simons, KT and Bonneau, R and Ruczinski, I and Baker, D}, year = {1999}, title = {Ab Initio Protein Structure Prediction of Casp Iii Targets Using Rosetta} , } @article{Singh2005, author = {Singh, GB and Singh, H}, title = {Functional proteomics with biolinguistic methods}, year = {2005}, volume = {24}, issue = {3}, pages = {73-80}, journal = {IEEE Engineering in Medicine and Biology Magazine} } @article{Slovic2004, author = {Slovic, AM and Kono, H and Lear, JD and Saven, JG and DeGrado, WF}, year = {2004}, title = {Computational Design of Water-Soluble Analogues of the Potassium Channel Kcsa}, journal = {Proc Natl Acad Sci U S A}, volume = {101}, issue = {7}, pages = {1828-33} } @article{Slovic2003, author = {Slovic, AM and Summa, CM and Lear, JD and DeGrado, WF}, year = {2003}, title = {Computational Design of a Water-Soluble Analog of Phospholamban}, journal = {Protein Sci}, volume = {12}, issue = {2}, pages = {337-48} } @article{Sonnhammer1998, author = {Sonnhammer, EL and von Heijne, G and Krogh, A}, year = {1998}, title = {A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences}, journal = {Proc Int Conf Intell Syst Mol Biol}, volume = {6}, issue = {2}, pages = {175-82} } @article{Stark2003, author = {Stark, A and Sunyaev, S and Russell, RB}, year = {2003}, title = {A Model for Statistical Significance of Local Similarities in Structure}, journal = {J Mol Biol}, volume = {326}, issue = {5}, pages = {1307-16} } @article{Strader1995, author = {Strader, CD and Fong, TM and Graziano, MP and Tota MR}, title = {The family of G-protein-coupled receptors}, year = {1995}, journal = {FASEB J}, volume = 9, issue = 9, pages = {745-54} } @article{Strait1996, author = {Strait, BJ and Dewey, TG}, year = {1996}, title = {The Shannon Information Entropy of Protein Sequences}, journal = {Biophys J}, volume = {71}, issue = {1}, pages = {148-55.} } @ARTICLE{Stuart2002, AUTHOR = {Stuart, GW and Moffett, K and Baker, S}, TITLE = {Integrated gene and species phylogenies from unaligned whole genome protein sequences}, JOURNAL = {Bioinformatics}, YEAR = {2002}, volume = {18}, number = {1}, pages = {100-8} } @article{Sugiyama2003, journal = {Protein Eng}, year = {2003}, volume = {16}, issue = {7}, pages = {479-88}, title = {Identification of transmembrane protein functions by binary topology patterns}, author = {Sugiyama, Y and Polulyakh, N and Shimizu, T} } @article{Sundararajan1996, author = {Sundararajan, V and Sunaina}, year = {1996}, title = {The Shannon Information Entropy of Protein Sequences}, journal = {Biophys J}, volume = {71}, issue = {1}, pages = {148-55.} } @article{Sunyaev1997, author = {Sunyaev, S and Kuznetsov, E and Rodchenkov, I and Tumanyan, V}, year = {1997}, title = {Protein Sequence-Structure Compatibility Criteria in Terms of Statistical Hypothesis Testing}, journal = {Protein Eng}, volume = {10}, issue = {6}, pages = {635-46} } @conference{Tan1996, author = {Tan, BT and Fu, M and Spray, A and Dermody, P}, year = {1996}, title = {The Use of Wavelet Transforms in Phoneme Recognition}, booktitle = {ICSLP96: Fourth International Conference on Spoken Language Processing}, location = {}, pages = {635-46} } @article{Taylor2002, author = {Taylor, WR and Heringa, J and Baud, F and Flores, TP}, year = {2002}, title = {A Fourier Analysis of Symmetry in Protein Structure}, journal = {Protein Eng}, volume = {15}, issue = {2}, pages = {79-89} } @article{Thomas2002, author = {Thomas, A and Meurisse, R and Brasseur, R}, year = {2002}, title = {Aromatic Side-Chain Interactions in Proteins. Ii. Near- and Far-Sequence Phe-X Pairs}, journal = {Proteins}, volume = {48}, issue = {4}, pages = {635-44} } @article{Thomas2002, author = {Thomas, A and Meurisse, R and Charloteaux, B and Brasseur, R}, year = {2002}, title = {Aromatic Side-Chain Interactions in Proteins. I. Main Structural Features}, journal = {Proteins}, volume = {48}, issue = {4}, pages = {628-34} } @article{Tomovic2006, author = {Tomovic, A and Janicic, P and Keselj, V}, year = {2006}, title = {n-gram-based classification and unsupervised hierarchical clustering of genome sequences}, pages = {137-53}, journal = {Comput Methods Programs Biomed}, issue = {2}, volume = {81} } @misc{Troyanskaya2002, author = {Troyanskaya, OG and Arbell, O and Koren, Y and Landau, GM and Bolshoy, A}, year = {2002}, title = {Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity} , } @conference{Treutlein1993, author = {Truetlein, HR and Lemmon, MA and Engelman, DM and Brunger, AT}, title = {Simulation of helix association in membranes: modeling a Glycophorin A transmembrane domain}, booktitle = {Proc. of the Twenty-Sixth Hawaii International Conference on System Sciences}, year = {1993}, location = {Hawaii} } @article{Tseitin1999, author = {Tseitin, VM and Nikiforovich, GV}, title = {Isolated transmembrane helices arranged across a membrane: computational studies}, journal = {Protein Eng}, year = {1999}, volume = {12}, issue = {4}, pages = {305-11} } @article{Tsonis1997, author = {Tsonis, AA and Elsner, JB and Tsonis, PA}, year = {1997}, title = {Is DNA a Language?}, journal = {J Theor Biol}, volume = {184}, issue = {1}, pages = {25-9.} } @article{Tuffery1994, author = {Tuffery, P and Etchebest, C and Popot, JL and Lavery, R}, year = {1994}, title = {Prediction of the Positioning of the Seven Transmembrane Alpha-Helices of Bacteriorhodopsin. A Molecular Simulation Study}, journal = {J Mol Biol}, volume = {236}, issue = {4}, pages = {1105-22} } @article{Tusnady2001, author = {Tusnady, GE and Simon, I}, year = {2001}, title = {The Hmmtop Transmembrane Topology Prediction Server}, journal = {Bioinformatics}, volume = {17}, issue = {9}, pages = {849-50} } @article{Venter2001, author = {Venter, JC and Adams, MD and Myers, EW and Li, PW and Mural, RJ and Sutton, GG and Smith, HO and Yandell, M and Evans, CA and Holt, RA and Gocayne, JD and Amanatides, P and Ballew, RM and Huson, DH and Wortman, JR and Zhang, Q and Kodira, CD and Zheng, XH and Chen, L and Skupski, M and Subramanian, G and Thomas, PD and Zhang, J and Gabor Miklos, GL and Nelson, C and Broder, S and Clark, AG and Nadeau, J and McKusick, VA and Zinder, N and Levine, AJ and Roberts, RJ and Simon, M and Slayman, C and Hunkapiller, M and Bolanos, R and Delcher, A and Dew, I and Fasulo, D and Flanigan, M and Florea, L and Halpern, A and Hannenhalli, S and Kravitz, S and Levy, S and Mobarry, C and Reinert, K and Remington, K and Abu-Threideh, J and Beasley, E and Biddick, K and Bonazzi, V and Brandon, R and Cargill, M and Chandramouliswaran, I and Charlab, R and Chaturvedi, K and Deng, Z and Di Francesco, V and Dunn, P and Eilbeck, K and Evangelista, C and Gabrielian, AE and Gan, W and Ge, W and Gong, F and Gu, Z and Guan, P and Heiman, TJ and Higgins, ME and Ji, RR and Ke, Z and Ketchum, KA and Lai, Z and Lei, Y and Li, Z and Li, J and Liang, Y and Lin, X and Lu, F and Merkulov, GV and Milshina, N and Moore, HM and Naik, AK and Narayan, VA and Neelam, B and Nusskern, D and Rusch, DB and Salzberg, S and Shao, W and Shue, B and Sun, J and Wang, Z and Wang, A and Wang, X and Wang, J and Wei, M and Wides, R and Xiao, C and Yan, C and Yao, A and Ye, J and Zhan, M and Zhang, W and Zhang, H and Zhao, Q and Zheng, L and Zhong, F and Zhong, W and Zhu, S and Zhao, S and Gilbert, D and Baumhueter, S and Spier, G and Carter, C and Cravchik, A and Woodage, T and Ali, F and An, H and Awe, A and Baldwin, D and Baden, H and Barnstead, M and Barrow, I and Beeson, K and Busam, D and Carver, A and Center, A and Cheng, ML and Curry, L and Danaher, S and Davenport, L and Desilets, R and Dietz, S and Dodson, K and Doup, L and Ferriera, S and Garg, N and Gluecksmann, A and Hart, B and Haynes, J and Haynes, C and Heiner, C and Hladun, S and Hostin, D and Houck, J and Howland, T and Ibegwam, C and Johnson, J and Kalush, F and Kline, L and Koduru, S and Love, A and Mann, F and May, D and McCawley, S and McIntosh, T and McMullen, I and Moy, M and Moy, L and Murphy, B and Nelson, K and Pfannkoch, C and Pratts, E and Puri, V and Qureshi, H and Reardon, M and Rodriguez, R and Rogers, YH and Romblad, D and Ruhfel, B and Scott, R and Sitter, C and Smallwood, M and Stewart, E and Strong, R and Suh, E and Thomas, R and Tint, NN and Tse, S and Vech, C and Wang, G and Wetter, J and Williams, S and Williams, M and Windsor, S and Winn-Deen, E and Wolfe, K and Zaveri, J and Zaveri, K and Abril, JF and Guigo, R and Campbell, MJ and Sjolander, KV and Karlak, B and Kejariwal, A and Mi, H and Lazareva, B and Hatton, T and Narechania, A and Diemer, K and Muruganujan, A and Guo, N and Sato, S and Bafna, V and Istrail, S and Lippert, R and Schwartz, R and Walenz, B and Yooseph, S and Allen, D and Basu, A and Baxendale, J and Blick, L and Caminha, M and Carnes-Stine, J and Caulk, P and Chiang, YH and Coyne, M and Dahlke, C and Mays, A and Dombroski, M and Donnelly, M and Ely, D and Esparham, S and Fosler, C and Gire, H and Glanowski, S and Glasser, K and Glodek, A and Gorokhov, M and Graham, K and Gropman, B and Harris, M and Heil, J and Henderson, S and Hoover, J and Jennings, D and Jordan, C and Jordan, J and Kasha, J and Kagan, L and Kraft, C and Levitsky, A and Lewis, M and Liu, X and Lopez, J and Ma, D and Majoros, W and McDaniel, J and Murphy, S and Newman, M and Nguyen, T and Nguyen, N and Nodell, M and Pan, S and Peck, J and Peterson, M and Rowe, W and Sanders, R and Scott, J and Simpson, M and Smith, T and Sprague, A and Stockwell, T and Turner, R and Venter, E and Wang, M and Wen, M and Wu, D and Wu, M and Xia, A and Zandieh, A and Zhu, X}, year = {2001}, title = {The Sequence of the Human Genome}, journal = {Science}, volume = {291}, issue = {5507}, pages = {1304-51.} } @book{Voet1995, author = {Voet, D and Voet, JG}, year = {1995}, title = {Biochemistry}, publisher = {J. Wiley \& Sons} } @article{Vonderviszt1986, author = {Vonderviszt, F, Matrai, G and Simon, I}, year = {1986}, title = {Characteristic Sequential Residue Environment of Amino Acids in Proteins}, journal = {Int J Pept Protein Res}, volume = {27}, issue = {5}, pages = {483-92} } @article{vonHeijne1979, author = {von Heijne, G and Blomberg, C}, year = {1979}, title = {Trans-membrane translocation of proteins. The direct transfer model}, journal = {Eur J Biochem}, volume = {97}, issue = {1}, pages = {175-181} } @article{vonHeijne1992, author = {von Heijne, G}, year = {1992}, title = {Membrane Protein Structure Prediction. Hydrophobicity Analysis and the Positive-inside Rule}, journal = {J Mol Biol}, volume = {225}, issue = {2}, pages = {487-94} } @misc{Vries2004, author = {Vries, J and Munshi, R and Tobi, D and Klein-Seetharaman, J and Benos, PV and Bahar, I}, year = {2004}, title = {A Sequence Alignment-Independent Method for Protein Classification} , } @article{Weiss1993, author = {Weiss, SM and Cohen, DM and Indurkhya, N}, year = {1993}, title = {Transmembrane Segment Prediction from Protein Sequence Data}, journal = {Proc Int Conf Intell Syst Mol Biol}, volume = {1}, issue = {2}, pages = {420-8} } @article{Weiss2000, author = {Weiss, O, Jimenez-Montano, MA and Herzel, H}, yearr = {2000}, title = {Information Content of Protein Sequences}, journal = {J Theor Biol}, volume = {206}, issue = {3}, pages= {379-86} } @misc{Weisser2004, author = {Weisser, D and Klein-Seetharaman, J}, year = {2004}, title = {Identification of Fundamental Building Blocks in Protein Sequences Using Statistical Association Measures} , } @article{White1994, author = {White, SH}, year = {1994}, title = {The Evolution of Proteins from Random Amino Acid Sequences: Ii. Evidence from the Statistical Distributions of the Lengths of Modern Protein Sequences}, journal = {J Mol Evol}, volume = {38}, issue = {4}, pages = {383-94} } @article{White1994AR, author = {White, SH}, year = {1994}, title = {Global Statistics of Protein Sequences: Implications for the Origin, Evolution, and Prediction of Structure}, journal = {Annu Rev Biophys Biomol Struct}, volume = {23}, issue = {4}, pages = {407-39} } @article{White1990, author = {White, SH and Jacobs, RE}, year = {1990}, title = {Statistical Distribution of Hydrophobic Residues Along the Length of Protein Chains. Implications for Protein Folding and Evolution}, journal = {Biophys J}, volume = {57}, issue = {4}, pages = {911-21} } @article{White1993, author = {White, SH and Jacobs, RE}, year = {1993}, title = {The Evolution of Proteins from Random Amino Acid Sequences. I. Evidence from the Lengthwise Distribution of Amino Acids in Modern Protein Sequences}, journal = {J Mol Evol}, volume = {36}, issue = {1}, pages = {79-95} } @article{Whitehead1986, author = {Whitehead, PR and Jacobs, D and Brown, NL}, year = {1986}, title = {Restriction Endonucleases from Herpetosiphon Giganteus: An Example of the Evolution of DNA Recognition Specificity?}, journal = {Nucleic Acids Res}, volume = {14}, issue = {17}, pages = {7031-45} } @misc{Wu1992, author = {Wu, C and Whitson, G and McLarty, J and Ermongkonchai, A and Chang, TC}, year = {1992}, title = {Protein Classification Artificial Neural System} , } @conference{Wu2000, author = {Wu, J and Zheng, F}, year = {2000}, title = {On Enhancing Katz-Smoothing Based Back-Off Language Model}, booktitle = {ICSLP’00: Conference on Spoken Language Processing}, location = {}, pages = {7031-45} } @article{Yu2003, author = {Yu, CH and Pomes R}, title = {Functional dynamics of ion channels: modulation of proton movement by conformational switches}, journal = {J Am Chem Soc}, year = {2003}, volume = 125, issue = 45, pages = {13890-4} } @article{Yuan2002, author = {Yuan, Z and Teasdale, RD}, year = {2002}, title = {Prediction of Golgi Type Ii Membrane Proteins Based on Their Transmembrane Domains}, journal = {Bioinformatics}, volume = {18}, issue = {8}, pages = {1109-15} } @article{Zbilut2003, author = {Zbilut, JP and Colosimo, A and Conti, F and Colafranceschi, M and Manetti, C and Valerio, M and Webber, CL and Jr. and Giuliani, A}, year = {2003}, title = {Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by Nonlinear Signal Analysis of Acylphosphatase and Abeta(1-40)}, journal = {Biophys J}, volume = {85}, issue = {6}, pages = {3544-57} } @article{Zhai2001, author = {Zhai, Y and Saier, MH, Jr.}, year = {2001}, title = {A Web-Based Program (What) for the Simultaneous Prediction of Hydropathy, Amphipathicity, Secondary Structure and Transmembrane Topology for a Single Protein Sequence}, journal = {J Mol Microbiol Biotechnol}, volume = {3}, issue = {4}, pages = {501-2} } @article{Zhang2001, author = {Zhang, NR}, year = {2001}, title = {Markov Models for Classification of Protein Helices}, journal = {Biochemistry}, volume = {218}, issue = {4}, pages = {501-2} } @inproceedings{Zhang2005, author = {Zhang, B and Chen, Z and Murphey, YL}, title = {Protein Secondary Structure Prediction Using Machine Learning}, year = {2005}, booktitle = {Proceedings of International Joint Conference on Neural Networks}, } @article{Zhou2005, author = {Zhou, H and Zhang, C and Liu, S and Zhou, Y}, year = {2005}, title = {Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations}, journal = {Nucleic Acids Res}, volume = {33}, issue = {web-server issue}, pages = {W193-197} } @article{Zhorov2004, author = {Zhorov, BS and Tikhonov, DB}, title = {Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action}, journal = {J Neurochem}, year = 2004, volume = 88, issue = 4, pages = {782-99} } @article{Zhou2004, author = {Zhou, Y and Mishra, B}, title = {Models of Genome Evolution}, year = {2004}, journal = {Lecture Notes in Computer Science}, pages = {287--304} } @article{Zhu1996, author = {Zhu, ZY and Blundell, TL}, year = {1996}, title = {The Use of Amino Acid Patterns of Classified Helices and Strands in Secondary Structure Prediction}, journal = {J Mol Biol}, volume = {260}, issue = {2}, pages = {261-76} } @conference{Zipf1932, author = {Zipf, GK}, year = {1932}, title = {Selective Studies and the Principle of Relative Frequency in Language}, booktitle = {ICSLP’00: Conference on Spoken Language Processing}, location = {}, pages = {261-76} } @book{Berry1999, title = {Understanding Search Engines: Mathematical Modeling and Text Retrieval}, author = {Berry, MW and Browne, M}, publisher = {Society for Industrial & Applied}, year = {1999} } @article{Ramasarma1996, author = {Ramasarma, T}, title = {Transmembrane domains participate in functions of integral membrane proteins},year = {1996},journal = {Indian J Biochem Biophys}, volume = {33}, issue = 1, pages = {20-9}} @article{Ubarretxena-Belandia2001, author = {Ubarretxena-Belandia, I and Engelman, DM}, title = {Helical membrane proteins: diversity of functions in the context of simple architecture},year = {2001}, journal = {Curr Opin Struct Biol}, volume = {11}, issue = {3}, pages = {370-6}} @article{Chen2004, author = {Chen, D and Zhao, M and Harris, SE and Mi, Z}, title = {Signal transduction and biological functions of bone morphogenetic proteins}, year = {2004},journal = {Front Biosci}, volume = {9}, pages = {349-58}} @article{Kopecek2001, author = {Kopecek, P and Altmannova, K and Weigl, E}, title = {Stress proteins: nomenclature, division and functions}, year = {2001}, journal = {Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub}, volume = {145}, issue = 2, pages = {39-47} } @article{Kanoh1997, author = {Kanoh, H and Kai, M and Wada, I}, title = {Phosphatidic acid phosphatase from mammalian tissues: discovery of channel-like proteins with unexpected functions}, year = {1997},journal = {Biochim Biophys Acta}, volume = {1348}, issue = {1-2}, pages = {56-62}} @article{Filipek2003ARB, author = {Filipek, S and Teller, DC and Palczewski, K and Stenkamp, R}, title = {The crystallographic model of rhodopsin and its use in studies of other G protein-coupled receptors}, year = {2003},journal = {Annu Rev Biophys Biomol Struct}, volume = {32}, pages = {375-97}} @article{Ballesteros2001, author = {Ballesteros, J and Palczewski, K}, title = {G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin},year = {2001}, journal = {Curr Opin Drug Discov Devel}, volume = {4}, issue = {5}, pages = {561-74}} @article{spencer2002, author = {Spencer, RH and Rees, DC}, title = {The alpha-helix and the organization and gating of channels}, year = {2002}, journal = {Annu Rev Biophys Biomol Struct}, volume = {31}, pages = {207-33} } @article{Arkin1997, author = {Arkin, IT and Brunger, AT and Engelman, DM}, title = {Are there dominant membrane protein families with a given number of helices?}, year = {1997},journal = {Proteins}, volume = {28}, issue = {4}, pages = {465-6} } @article{Wallin1998, author = {Wallin, E and von Heijne, G}, title = {Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms}, year = {1998},journal = {Protein Sci}, volume = {7}, issue = 4, pages = {1029-38}} @article{Jones1994, author = {Jones, DT and Taylor, WR and Thornton, JM}, title = {A model recognition approach to the prediction of all-helical membrane protein structure and topology}, year = {1994},journal = {Biochemistry}, volume = {33}, issue = {10}, pages = {3038-49}} @article{White1999, author = {White, SH and Wimley, WC}, title = {Membrane protein folding and stability: physical principles}, year = {1999},journal = {Annu Rev Biophys Biomol Struct}, volume = {28}, pages = {319-65}} @article{Jayasinghe2001MTopo, author = {Jayasinghe, S and Hristova, K and White, SH}, title = {MPtopo: A database of membrane protein topology}, year = {2001},journal = {Protein Sci}, volume = {10}, issue = 2, pages = {455-8}} @book{thecell, title = {Molecular Biology of the Cell}, author = {Alberts, B and Johnson, A and Lewis, J and Raff, M and Roberts, K and Walter, P}, year = {2002}, edition = {4th}, publisher = {Garland Science} } @article{Wimley1996, author = {Wimley, WC and White, SH}, title = {Experimentally determined hydrophobicity scale for proteins at membrane interfaces}, year = {1996},journal = {Nat Struct Biol}, volume = {3}, issue = {10}, pages = {842-8}} @article{Rees1989, author = {Rees, DC and DeAntonio, L and Eisenberg, D}, title = {Hydrophobic organization of membrane proteins}, year = {1989},journal = {Science}, volume = {245}, issue = {4917}, pages = {510-3}} @article{Engelman1980, author = {Engelman, DM and Zaccai, G}, title = {Bacteriorhodopsin is an inside-out protein}, year = {1980},journal = {Proc Natl Acad Sci U S A}, volume = {77}, issue = {10}, pages = {5894-8}} @article{Eilers2000, author = {Eilers, M and Shekar, SC and Shieh, T and Smith, SO and Fleming, PJ}, title = {Internal packing of helical membrane proteins}, year = {2000},journal = {Proc Natl Acad Sci U S A}, volume = {97}, issue = {11}, pages = {5796-801}} @article{Eyre2004, author = {Eyre, TA and Partridge, L and Thornton, JM}, title = {Computational analysis of alpha-helical membrane protein structure: Implications for the prediction of 3D structural models}, year = {2004}, journal = {Protein Eng Des Sel}, volume={Advanced access publication} } @article{Mitaku1999, author = {Mitaku, S and Hirokawa, T}, title = {Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length}, year = {1999},journal = {Protein Eng}, volume = {12}, issue = {11}, pages = {953-7}} @article{Senes2000, author = {Senes, A and Gerstein, M and Engelman, DM}, title = {Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions}, year = {2000},journal = {J Mol Biol}, volume = {296}, issue = 3, pages = {921-36}} @article{Samatey1995, author = {Samatey, FA and Xu, C and Popot, JL}, title = {On the distribution of amino acid residues in transmembrane alpha-helix bundles}, year = {1995},journal = {Proc Natl Acad Sci U S A}, volume = {92}, issue = {10}, pages = {4577-81}} @article{Tusnady1998, author = {Tusnady, GE and Simon, I}, title = {Principles governing amino acid composition of integral membrane proteins: application to topology prediction}, year = {1998},journal = {J Mol Biol}, volume = {283}, issue = 2, pages = {489-506}} @article{Claros1994, author = {Claros, MG and von Heijne, G}, title = {TopPred II: an improved software for membrane protein structure predictions}, year = {1994},journal = {Comput Appl Biosci}, volume = {10}, issue = 6, pages = {685-6}} @article{Hirakawa1997, author = {Hirakawa, H and Kuhara, S}, title = {Prediction of Hydrophobic Cores of Proteins Using Wavelet Analysis}, year = {1997},journal = {Genome Inform Ser Workshop Genome Inform}, volume = {8}, pages = {61-70}} @article{Hirakawa1999, author = {Hirakawa, H and Muta, S and Kuhara, S}, title = {The hydrophobic cores of proteins predicted by wavelet analysis}, year = {1999},journal = {Bioinformatics}, volume = {15}, issue = 2, pages = {141-8}} @article{deTrad2002, author = {de Trad, CH and Fang, Q and Cosic, I}, title = {Protein sequence comparison based on the wavelet transform approach}, year = {2002}, journal = {Protein Eng}, volume = {15}, issue = 3, pages = {193-203}} @article{Klabunde2002, author = {Klabunde, T and Hessler, G}, title = {Drug design strategies for targeting G-protein-coupled receptors}, year = {2002},journal = {Chembiochem}, volume = {3}, issue = 10, pages = {928-44}} @article{Fredriksson2003, author = {Fredriksson, R and Lagerstrom, MC and Lundin, LG and Schioth, HB}, title = {The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints}, year = {2003}, journal = {Mol Pharmacol}, volume = {63}, issue = 6, pages = {1256-72} } @article{Eisenberg1984, author = {Eisenberg, D and Weiss, RM and Terwilliger, TC}, title = {The hydrophobic moment detects periodicity in protein hydrophobicity}, year = {1984}, journal = {Proc. Natl. Acad. Sci.}, volume = {81}, pages = {140-144} } @conference{Pattini2002, author = {Pattini, L and Riva, L and Cerutti, S}, title = {A wavelet based method to predict the alpha helix content in the secondary structure of globular proteins}, year = {2002}, booktitle = {IEEE} } @article{Krishnan2004, author = {Krishnan, A and Li, KB and Issac, P}, title = {Rapid detection of conserved regions in protein sequences using wavelets}, journal = {Silico Biol}, volume = {4}, issue = {2} } @article{Needleman1970, author = {Needleman, SB and Wunsch, CD}, title = {A general method applicable to the search for similarities in the amino acid sequence of two proteins}, year = {1970},journal = {J Mol Biol}, volume = {48}, issue = 3, pages = {443-53}} @article{Edelman1993, author = {Edelman, J}, title = {Quadratic minimization of predictors for protein secondary structure. Application to transmembrane alpha-helices}, year = {1993},journal = {J Mol Biol}, volume = {232}, issue = 1, pages = {165-91}} @article{Hirokawa1998, author = {Hirokawa, T and Boon-Chieng, S and Mitaku, S}, title = {SOSUI: classification and secondary structure prediction system for membrane proteins}, year = {1998},journal = {Bioinformatics}, volume = {14}, issue = {4}, pages = {378-9}} @article{Fariselli1996, author = {Fariselli, P and Casadio, R}, title = {HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins}, year = {1996},journal = {Comput Appl Biosci}, volume = {12}, issue = 1, pages = {41-8}} @article{Ikeda2003, author = {Ikeda, M and Arai, M and Okuno, T and Shimizu, T}, title = {TMPDB: a database of experimentally-characterized transmembrane topologies}, year = {2003},journal = {Nucleic Acids Res}, volume = {31}, issue = 1, pages = {406-9}} @article{Nilsson2000, author = {Nilsson, J and Persson, B and von Heijne, G}, title = {Consensus predictions of membrane protein topology}, year = {2000},journal = {FEBS Lett}, volume = {486}, issue = 3, pages = {267-9}} @article{Viklund2004, author = {Viklund, H and Elofsson, A}, title = {Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information}, year = {2004},journal = {Protein Sci}, volume = {13}, issue = 7, pages = {1908-17}} @article{Moller2000, author = {Moller, S and Kriventseva, EV and Apweiler, R}, title = {A collection of well characterised integral membrane proteins},\ year = {2000},journal = {Bioinformatics}, volume = {16}, issue = 12, pages = {1159-60}} @article{Kernytsky2003, author = {Kernytsky, A and Rost, B}, title = {Static benchmarking of membrane helix predictions}, year = {2003},journal = {Nucleic Acids Res}, volume = {31}, issue = 13, pages = {3642-4} } @article{Shepherd2003, author = {Shepherd, AJ and Gorse, G and Thornton, JM}, title = {A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks}, journal = {Proteins}, year = {2003}, volume ={50}, issue = {2}, pages = {290-302} } @article{Takeda2002, author = {Takeda, S and Kadowaki, S and Haga, T and Takaesu, H and Mitaku, S}, year = {2002}, title = {Identification of G Protein-Coupled Receptor Genes from the Human Genome Sequence}, journal = {FEBS Lett}, volume = {520}, issue = {1-3}, pages = {97-101} } @article{Imai2004, author = {Imai, T and Fujita, N}, year = {2004}, title = {Statistical Sequence Analyses of G-Protein-Coupled Receptors: Structural and Functional Characteristics Viewed with Periodicities of Entropy, Hydrophobicity, and Volume}, journal = {Proteins}, volume = {56}, issue = {4}, pages = {650-60} } @article{Sadka2005, author = {Sadka, T and Linial, M}, year = {2005}, title = {Families of Membranous Proteins Can Be Characterized by the Amino Acid Composition of Their Transmembrane Domains}, journal = {Bioinformatics}, volume = {21 Suppl 1}, issue = {13-15}, pages = {i378-86} } @article{Petersen2000, author = {Petersen, TN and Lundegaard, C and Nielsen, M and Bohr, H and Bohr, J and Brunak, S and Gippert, GP and Lund, O}, year = {2000}, title = {Prediction of Protein Secondary Structure at 80% Accuracy}, journal = {Proteins}, volume = {41}, issue = {1}, pages = {17-20} } @article{Ganapathiraju2004AB, author = {Ganapathiraju, M and Manoharan, V and Klein-Seetharaman, J}, year = {2004}, title = {Blmt: Statistical Sequence Analysis Using N-Grams}, journal = {Applied Bioinformatics}, volume = {3}, issue = {2-3}, pages = {193-200} } @article{Phoenix2002, author = {Phoenix, DA and Harris, F}, year = {2002}, title = {The Hydrophobic Moment and Its Use in the Classification of Amphiphilic Structures (Review)}, journal = {Mol Membr Biol}, volume = {19}, issue = {1}, pages = {1-10} } @misc{Zhang2000, author = {Zhang, N}, year = {2000}, title = {Periodicities in Sequence Residue Hydropathy and the Implications on Protein Folds}, } @article{Palczewski2000, author = {Palczewski, K and Kumasaka, T and Hori, T and Behnke, CA and Motoshima, H and Fox, BA and Le Trong, I and Teller, DC and Okada, T and Stenkamp, RE and Yamamoto, M and Miyano, M}, title = {Crystal structure of rhodopsin: A G protein-coupled receptor}, year = {2000}, journal = {Science}, volume = {289}, issue = {5480}, pages = {739-45} } @article{Taylor1986, author = {Taylor, WR}, year = {1986}, title = {The classification of amino acid conservation}, volume = {119}, issue = {2}, journal = {J Theor Biol}, pages = {205-18} } @ARTICLE{Hopp1981, AUTHOR = {Hopp, TP and Woods, KR}, TITLE = {Prediction of Protein Antigenic Determinants from Amino Acid Sequences}, JOURNAL = {PNAS}, YEAR = {1981}, volume = {78}, number = {6}, pages = {3824-3828} } @ARTICLE{Lawson1984, AUTHOR = {Lawson, EQ and Sadler, AJ and Harmatz, D and Brandau, DT and Micanovic, R and MacElroy, RD and Middaugh, CR}, TITLE = {A simple experimental model for hydrophobic interactions in proteins}, JOURNAL = {J Biol Chem}, YEAR = {1984}, volume = {259}, number = {5}, pages = {2910-2912} } @ARTICLE{Levitt1976, AUTHOR = {Levitt, M}, TITLE = {A simplified representation of protein conformations for rapid simulation of protein folding.}, JOURNAL = {J Mol Biol}, YEAR = {1976}, volume = {104}, number = {1}, pages = {59-107} } @ARTICLE{Nakashima1990, AUTHOR = {Nakashima H and Nishikawa, K and Ooi, T}, TITLE = {Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins}, JOURNAL = {Proteins}, YEAR = {1990}, volume = {8}, number = {2}, pages = {173-178} } @ARTICLE{Radzicka1988, AUTHOR = {Radzicka A, Wolfenden R}, TITLE = {Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution}, JOURNAL = {Biochemistry}, YEAR = {1988}, volume = {27}, number = {5}, pages = {1664-1670} } @ARTICLE{Roseman1988, AUTHOR = {Roseman, MA}, TITLE = {Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds}, JOURNAL = {J Mol Biol}, YEAR = {1988}, volume = {200}, number = {3}, pages = {513-522} } @ARTICLE{Sweet1983, AUTHOR = {Sweet, RM and Eisenberg, D}, TITLE = {Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure}, JOURNAL = {J Mol Biol}, YEAR = {1983}, volume = {171}, number = {4}, pages = {479-488} } @ARTICLE{Wolfenden1981, AUTHOR = {Wolfenden, R and Andersson, L and Cullis, PM and Southgate, CC}, TITLE = {Affinities of amino acid side chains for solvent water}, JOURNAL = {Biochemistry}, YEAR = {1981}, volume = {20}, number = {4}, pages = {849-855} }