Structural genomics is the largest contributor of novel structural leverage
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Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36:D419–D425. doi: 10.1093/nar/gkm993
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M et al (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:D115–D119. doi: 10.1093/nar/gkh131
Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL Jr, Fidelis K, Frank J et al (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14:1211–1217. doi: 10.1016/j.str.2006.06.005
Berman H, Henrick K, Nakamura H, Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301–D303. doi: 10.1093/nar/gkl971
Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA et al (2008) Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins. doi: 10.1002/prot.22287
Bhattacharya A, Wunderlich Z, Monleon D, Tejero R, Montelione GT (2008) Assessing model accuracy using the homology modeling automatically software. Proteins 70:105–118. doi: 10.1002/prot.21466
Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, et al. (2004) The status of structural genomics defined through the analysis of current targets and structures. Pac Symp Biocomput 9:375–386
Chandonia JM, Brenner SE (2005) Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58:166–179. doi: 10.1002/prot.20298
Chen L, Oughtred R, Berman HM, Westbrook J (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics 20:2860–2862. doi: 10.1093/bioinformatics/bth300
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823–826
Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23:2558–2565. doi: 10.1093/bioinformatics/btm377
Fraser-Liggett CM (2005) Insights on biology and evolution from microbial genome sequencing. Genome Res 15:1603–1610. doi: 10.1101/gr.3724205
Gerstein M, Edwards A, Arrowsmith CH, Montelione GT (2003) Structural genomics: current progress. Science 299:1663. doi: 10.1126/science.299.5613.1663a
Grant A, Lee D, Orengo C (2004) Progress towards mapping the universe of protein folds. Genome Biol 5:107. doi: 10.1186/gb-2004-5-5-107
Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C (2003) Recognizing the fold of a protein structure. Bioinformatics 19:1748–1759. doi: 10.1093/bioinformatics/btg240
Koh IYY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Narayanan E, Grana O, Valencia A, Sali A, Rost B (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 31:3311–3315. doi: 10.1093/nar/gkg619
Kopp J, Schwede T (2004) The SWISS-MODEL repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res 32:D230–D234. doi: 10.1093/nar/gkh008
Levitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104:3183–3188. doi: 10.1073/pnas.0611678104
Liu J, Rost B (2003) Domains, motifs, and clusters in the protein universe. Curr Opin Chem Biol 7:5–11. doi: 10.1016/S1367-5931(02)00003-0
Liu J, Rost B (2004) CHOP: parsing proteins into structural domains. Nucleic Acids Res 32:W569–W571. doi: 10.1093/nar/gkh481
Liu J, Hegyi H, Acton TB, Montelione GT, Rost B (2004) Automatic target selection for structural genomics on eukaryotes. Proteins 56:188–200. doi: 10.1002/prot.20012
Liu J, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25:849–851. doi: 10.1038/nbt0807-849
Marsden RL, Orengo CA (2008) Target selection for structural genomics: an overview. Methods Mol Biol 426:3–25. doi: 10.1007/978-1-60327-058-8_1
Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325. doi: 10.1146/annurev.biophys.29.1.291
Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A (2002) Reliability of assessment of protein structure prediction methods. Structure 10:435–440. doi: 10.1016/S0969-2126(02)00731-1
Moult J, Fidelis K, Rost B, Hubbard T, Tramontano A (2005) Critical assessment of methods of protein structure prediction (CASP)-round 6. Proteins 61:3–7. doi: 10.1002/prot.20716
Moult J, Fidelis K, Kryshtafovych A, Rost B, Hubbard T, Tramontano A (2007) Critical assessment of methods of protein structure prediction-round VII. Proteins 69(Suppl 8):3–9. doi: 10.1002/prot.21767
Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540
Nair R, Fajardo E, Fiser A, Godzik A, Jaroszewski L, Marsden R, Orengo C, Rost B (2008) Progress at PSI—milestones measuring the success of structural genomics in the USA. Columbia University, New York
Norvell JC, Berg JM (2007) Update on the protein structure initiative. Structure 15:1519–1522. doi: 10.1016/j.str.2007.11.004
Orengo CA, Michie AD, Jones DT, Swindells MB, Thornton JM (1997) CATH—a hierarchic classification of protein domain structures. Structure 5:1093–1108. doi: 10.1016/S0969-2126(97)00260-8
Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A et al (2004) MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32:D217–D222. doi: 10.1093/nar/gkh095
Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D et al (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34:D291–D295. doi: 10.1093/nar/gkj059
Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA (2007) CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLoS Comput Biol 3:e232. doi: 10.1371/journal.pcbi.0030232
Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56–68. doi: 10.1002/prot.340090107
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43. doi: 10.1038/nature02340
Watson JD, Todd AE, Bray J, Laskowski RA, Edwards A, Joachimiak A, Orengo CA, Thornton JM (2003) Target selection and determination of function in structural genomics. IUBMB Life 55:249–255. doi: 10.1080/1521654031000123385
Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C (2008) Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res 36:D414–D418. doi: 10.1093/nar/gkm1019