@Article{Hargbo:1999, author = {Jeanette Hargbo and Arne Elofsson}, title = {A study of hidden Markov models that use predicted secondary structures for fold recognition.}, journal = {Proteins}, year = 1999 } @Article{Abagyan:1997, author = {Ruben A. Abagyan and Serge Batalov}, title = {Do aligned sequences share the same fold?}, journal = {J. Mol. Biol.}, year = 1997, volume = 273, pages = {355-368} } @Article{Jones:1992, author = "Jones, D.T. and Taylor, W.R. and Thornton, J.M.", title = "A new appoach to protein fold recognition", journal = "Nature", year = 1992, volume = 358, pages = "86 -- 89" } @Article{Arvestad:1999, author = {Arvestad, L and Ivansson,L and Lagergren, J and Elofsson, A}, title = {On the structural and evolutionary significance of pairwise sequence alignments.}, journal = {Proteins}, year = {submitted}, OPTkey = {}, OPTvolume = {}, OPTnumber = {}, OPTpages = {}, OPTmonth = {}, OPTnote = {}, OPTannote = {} } @Article{Sander:1991, author = "Sander, C and Schneider, R", title = "Database of homology derived protein structures and the structural meaning of sequence alignment", journal = "Proteins", year = 1991, volume = 9, number = 9, pages = "56--68" } @Article{Park:1998, author = {Park, J and Karplus, K and Barrett, C and Hughey, R and Haussler, D and Hubbard, T and Chothia C}, title = {Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.}, journal = {J Mol Biol}, year = 1998, volume = 284, number = 4, pages = {1201--1210} } @Article{Sonnhammer:1997, key = "Sonnhammer:1997", author = "Sonnhammer, E L and Eddy, S R and Durbin, R", title = "Pfam: a Comprehensive database of protein domain families based on seed alignments", journal = "Proteins, Structure function and genetics ", year = "1997", volume = "28", pages = "405--420", OPTnumber = "3" } @Article{Park:1997, author = {Park, J and Teichmann, S.A. and Hubbard, T and Chothia, C}, title = {Intermediate sequences increase the detection of homology between sequences.}, journal = {J. Mol. Biol.}, year = 1997, volume = 273, number = 1, pages = {249--254} } @Article{Bairoch:1996, author = "Bairoch, A and Apweiler, R", title = "The SWISS-PROT protein sequence data bank and its new supplement TREMBL.", journal = "Nucleic Acids Res.", year = 1996, volume = 24, pages = "17--21" } @Article{Murzin:1995, author = "Murzin, A G and Brenner, S E and Hubbard, T and Chothia, C", title = "SCOP: a structural classification of proteins database for the investigation of sequences and structures", key = "Murzin:1995", journal = "J. Mol. Biol.", year = 1995, volume = 247, number = 4, pages = "536--540" } @Article{Lesk:1980, author = "Lesk, A.M. and Chithia, C", title = "How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins", journal = "J. Mol. Biol.", year = 1980, volume = 136, pages = "225--270" } @Article{Lesk:1986, author = "Chothia, C and Lesk, A.M.", title = "The relationship between the divergence of sequence and structure in proteins", journal = "EMBO J.", year = 1986, volume = 5, pages = "823--826" } @Article{Altschul:1997, author = "Altschul, SF and Madden, TL and Schaffer, AA and Zhang, J and Zhang, Z and Miller, W and Lipman, DJ", title = "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", journal = "Nucleic Acids Res.", year = "1997", volume = "25", number = "17", pages = "3389--3402", } @Article{Brenner:1998, author = "S. E. Brenner and C. Chothia and T. Hubbard", title = "Assessing sequence comparison methods with reliable structurally identified evolutionary relationships", journal = "Proc. Natl. Acad. Sci. USA", year = 1998, volume = 95, number = 11, pages = "6073--6078" } @Article{Pearson:1988, author = "Pearson, W R and Lipman, D J ", title = "Improved Tools for Biological Sequence Analysis", journal = "Proc. Natl. Acad. Sci. U.S.A.", year = 1988, volume = 85, pages = "2444--2448" } @Article{Pearson:1995, author = "W.R. Pearson", title = "Comparison of methods for searching protein sequence databases", journal = "Protein Sci.", year = 1995, volume = 4, pages = "1145--1160" } @Article{Holm:1997-dali, author = "Holm, L and Sander, C", title = "Touring protein fold space with Dali/FSSP", journal = "Nucl. Acid. Res.", year = 1998, volume = 26, number = 1, pages = "316--319" } @Misc{Abagyan:personal, author = "R. Abagyan", howpublished = "Personal communication", year = 1998 } @Misc{Rost:personal, author = "B. Rost", howpublished = "Personal communication", year = 1998 } @Article{Smith:1981, author = "Smith, T.F. and Waterman, M.S.", title = "Identification of common molecular subsequences", journal = "J. Mol. Biol.", year = 1981, volume = 147, pages = "195--197" } @Article{Needleman:1970, author = "Needleman, S.B. and Wunsch, C.D.", title = "A general method applicable to the search for similarities in the amino acid sequence of two proteins", journal = "J. Mol. Biol.", year = 1970, volume = 48, pages = "443--453" } @Article{Henikoff:1992, author = "Henikoff, S. and Henikoff, J.G.", title = "Amino acid substitution matrices from protein blocks", journal = "Proc. Natl. Acad. Sci. USA", year = 1992, volume = 89, pages = "10915--10919" } @Article{Gonnet:1992, author = "Gonnet, G.H. and CCohen, M.A. and Benner, S.A.", title = "Exhaustive matching of the entire protein sequence database", journal = "Science", year = 1992, volume = 256, pages = "1443--1445" } @InBook{Dayhoff:1978, author = "Dayhoff, M. and Schwartz, R.M. and Orcutt, B.C.", title = "Atlas of protein sequence and structure", chapter = "A model of evolutionary change in proteins. ", publisher = "National Biomedical Research Foundation", year = 1978, editor = "Dayhoff, M", pages = "345--352", volume = 5, number = 3, address = "Silver Spring, Maryland" } @Article{Karlin:1989, author = "Karlin, S and Blaisdell, BE and Mocarski, ES and Brendel, V", title = "A method to identify distinctive charge configurations in protein sequences, with application to human herpesvirus polypeptides", journal = "J. Mol. Biol.", year = 1989, volume = 205, number = 1, pages = "165--177" } @Article{Vingron:1995, author = "Vingron", title = "????", OPTcrossref = "", OPTkey = "", OPTjournal = "", year = "1995", OPTvolume = "", OPTnumber = "", OPTpages = "", OPTmonth = "", OPTnote = "", OPTannote = "" } @Article{Rost:1993, author = "B. Rost and C. Sander", title = "Prediction of protein secondary structure structure at better than 70\% accuracy", journal = "J. Mol. Biol.", year = 1993, pages = "584 -- 599" } @Article{Rice:1997a, author = "D. Rice and D. Eisenberg", title = "A 3{D}-1{D} substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence", journal = "J. Mol. Biol.", year = 1997, volume = 267, pages = "1026 -- 1038" } @Article{Fischer:1996, author = "D. Fischer and D. Eisenberg", title = "Protein fold recognition using sequence-derived predictions", journal = "Protein Sci.", year = 1996, volume = 5, number = 5, pages = "947 -- 955" } @Article{Rost:1997, author = "B Rost and R. Schneider and C. Sander", title = "Protein fold recognition by prediction-based threading", journal = "J. Mol. Biol.", year = "1997 ", volume = 270, number = 3, pages = "471 -- 480 " } @Article{Rice:1997b, author = "Rice, D and Fischer, D and Weiss, R and Eisenberg, D", title = "Fold assignments for amino acid sequences of the {C}{A}{S}{P}2 experiment", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "113 -- 122" } @Article{DiFranscesco:1997, author = "Di Francesco, V and Geetha, V. and Garnier, J. and Munson, P.J.", title = "Fold recognition using predicted secondary structure sequences and hidden {M}arkov models of proteins folds", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "123 -- 128" } @Article{Murzin:1997, author = "A.G. Murzin and A. Bateman", title = "Distant homology recognition using structural classification of proteins", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "105 -- 112" } @Article{Flockner:1997, author = "H. Flöckner and F. Domingues and M.J. Sippl", title = "Proteins folds from pair interactions: A blind test in fold recogition", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "129 -- 133" } @Article{Karplus:1997, author = "K. Karplus and K. Sjölander and C. Barrett and M. Cline and D. Haussler and R. Hughey and L. Holm and C. Sander", title = "Predicting structures using hidden {M}arkov models", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "134 -- 139" } @Article{Bowie:1991, author ="Bowie, James U. and Lüthy, Roland and Eisenberg, David", title ="A method to identify protein sequence that fold into a known three-dimensional structure", journal ="Science", year =1991, volume =253, pages ="164 -- 170" } @misc{hmmer, author = "Eddy, Sean R", title = "H{M}{M}{E}{R} -- Hidden {M}arkov model software URL: http://genome.wustl.edu/eddy/hmmer.html ", url = "http://genome.wustl.edu/eddy/hmm.html", year = 1997 } @Book{Durbin:1998, author = "R. Durbin and S. Eddy and A. Krogh and G. Mitchison", title = "Biological sequence analysis", publisher = "Cambridge University press", year = 1998, address= "Cambridge, UK" } @Article{Krogh:1994, author = "Krogh, A and Brown, M and Mian, I.S. and Sjölander, K and Haussler, D", title = "Hidden {M}arkov models in computational biology: applications to protein modeling", journal = "J. Mol. Biol.", year = 1994, volume = 235, pages = "1501 -- 1531" } @Article{CASP, author = "Moult, J. and Hubbard, T. and Bryant, S.H. and Fidelis, K. and J.T. Pedersen", title = "Critical assesment of methods of proteins structure predictions ({C}{A}{S}{P}): Round {I}{I}", journal = "Proteins, Suppl", year = 1997, volume = 1, number = 1, pages = "2 -- 6" } @Unpublished{Arvestad:1998, author = "L. Arvestad and L. Ivansson and J. Lagergren and A. Elofsson", title = "Identification of related proteins by pairwise sequence alignments", note = "Manuscript", year = 1998 } @Article{Frishman:1997, author = "D. Frishman and P. Argos", title = "Seventy-five percent accuracy in protein secondary structure prediction", journal = "Proteins", year = 1997, volume = 27, number = 3, pages = "329 -- 335" } @inbook{Haussler:1993, author = "Haussler, D and Krogh, A and Mian, I.S. and Sjölander, K.", title = "Protein modeling using hidden {M}arkov models: Analysis of globins", year = 1993, volume = 1, pages = "792 -- 802", booktitle = "{``}Hawaii International Conference on Systems Science{``}", organization = "Hawaii International Conference on Systems Science", publisher = "IEEE Computer Society Press", address = "Los Alamitos, CA" } @InProceedings{Haussler:1993old, author = "Haussler, D and Krogh, A and Mian, I.S. and Sjölander, K.", title = "Protein modeling using hidden Markov models: Analysis of globins", year = 1993, volume = 1, pages = "792 -- 802", booktitle = "{\" }Hawaii International Conference on Systems Science", organization = "Hawaii International Conference on Systems Science", publisher = "IEEE Computer Society Press", address = "Los Alamitos, CA" } @Book{Rabiner:1986, author = "Rabiner, L.R. and Juang, B.H.", title = "An introduction to hidden {M}arkov models", publisher = "IEEE ASSP Magazine, January. 4-15", year = 1986, address = "Los Alamitos, CA" } @Article{Dayhoff:1983, author = "Dayhoff, M.O. and Barker, W.C. and Hunt, L.T.", title = "Establishing homologies in protein sequences", journal = "Meth. Enzymol.", year = 1983, volume = 91, pages = 254 } @Article{Park:1995, author = {Hubbard, T .J.and Park, J.}, title = {Fold recognition and ab initio structure predictions using hidden Markov models andbeta-strand pair potentials.}, journal = {Proteins}, year = 1995, volume = 23, pages = {398 -- 402} } @InProceedings{hmmgene, author = {Krogh, A}, title = { Two methods for improving performance of an HMM and their application for gene finding}, booktitle = {Proc. of Fifth Int. Conf. on Intelligent Systems for Molecular Biology}, pages = {179 -- 186}, year = 1997, editor = {Gaasterland, T. et al}, publisher = {AAA1 Press} } @InProceedings{tmhmm, author = {Sonnhammer, E. and von Heijne, G. and Krogh, A.}, title = {A hidden Markov model for predicting transmembrane helices in protein sequences. }, booktitle = {Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology. }, pages = {to appear }, year = 1998, publisher = {AAA1 Press} } @Article{Elofsson:1996, author = {Elofsson, A. and Fischer, D. and Rice, D.W. and Le Grand, S.M. and Eisenberg D.}, title = {A study of combined structure/sequence profiles.}, journal = {Fold Des}, year = 1996, volume = 1, number = 6, pages = {451 -- 461} } @Article{Gribskov:1987, author = {Gribskov, M and McLachlan, A.D. and Eisenberg, D}, title = {Profile analysis: detection of distantly related proteins.}, journal = {Proc Natl Acad Sci U S A}, year = 1987, volume = 84, number = 13, pages = {4355--4358} } @Article{Gerstein:1998, author = {Gerstein, M and Levitt, M}, title = {Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins.}, journal = {Protein Sci}, year = 1998, volume = 7, number = 2, pages = {445--456} } @Article{Holm:1997, author = {L. Holm and C. Sander}, title = {An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.}, journal = {Proteins}, year = 1997, volume = 28, number = 1, pages = {72--82} } @Article{Karplus:1998, author = {Kevin Karplus and Christian Barrett and Richard Hughey}, title = {Hidden Markov Models for Detecting Remote Protein Homologies}, journal = {Bioinformatics}, year = 1998, volume = 14, number = 10, pages = {846--856} } @Article{Orengo:1997, author = {Orengo, C.A: and Michi, A.D. and Jones, S. and Jones, D.T. and Swindelss, M.B. and Thornton, J.M.}, title = {CATH - A hierarchical classification of protein domain structures.}, journal = {Structure}, year = 1997, volume = 5, pages = {1093--1108} } @Article{Salamov:1999, author = {Asaf A. Salamov and Mikiko Suwa and Christine A. Orengo and Mark B. Swindells}, title = {Genome analysis: Assigning protein coding regions ato three-dimensional structures}, journal = {Protein Science}, year = 1999, volume = 8, pages = {771--777} } @Article{Sheridan:1985, author = {Sheridan, R.P. and Dixon, J.S. and Venkataraghavan, R.}, title = {Gnerating palusible protein folds by secondary structure similarity. }, journal = {Int. J. Pept. Protein Res.}, year = 1985, volume = 25, pages = {132--143} }