Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014

Сравнительное моделирование структуры белков
Литература

Abagyan R, Totrov М (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235:983-1002

Alber F, Dokudovskaya S, Veenhoff LM, et al. (2007a) Determining the architectures of macromolecular assemblies. Nature 450:683-694

Alber F, Dokudovskaya S, Veenhoff LM, et al. (2007b) The molecular architecture of the nuclear pore complex. Nature 450:695-701

Alber F, Forster F, Korkin D, et al. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443—477

AI Lazikani B, Sheinerman FB, Honig В (2001) Combining multiple structure and sequence alignments to improve sequence detection and alignment: application to the SH2 domains of Janus kinases. Proc Natl Acad Sci USA 98:14796

Altschul SF, Madden TL, Schaffer AA, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402

Andreeva A, Howorth D, Chandonia JM, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36:D419-425

Apostolico A, Giancarlo R (1998) Sequence alignment in molecular biology. J Comput Biol 5:173-196

Apweiler R, Bairoch A, Wu CH (2004) Protein sequence databases. Curr Opin Chem Biol 8:76-80

Aszodi A, Taylor WR (1994) Secondary structure formation in model polypeptide chains. Protein Eng 7:633-644

Aszodi A, Taylor WR (19%) Homology modelling by distance geometry. Fold Des 1:325-334 Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294:93-96

Barrientos LGt, Campos-Olivas R, Louis JM, et al. (2001) 1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N. J Biomol NMR 19:289-290

Battey JN, Корр J, Bordoli L, et al. (2007) Automated server predictions in CASP7. Proteins 69(Suppl 8):68—82

Becker OM, Dhanoa DS, Marantz Y, et al. (2006) An integrated in silico 3D model-driven discovery of a novel, potent, and selective amidosulfonamide 5-HT1A agonist (PRX-00023) for the treatment of anxiety and depression. J Med Chem 49:3116-3135

Berman H, Henrick K, Nakamura H, et al. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35:D301-303

Blake JD, Cohen FE (2001) Pairwise sequence alignment below the twilight zone. J Mol Biol 307:721-735

Blundell TL, Sibanda BL, Sternberg MJ, et al. (1987) Knowledge-based prediction of protein structures and the design of novel molecules. Nature 326:347-352

Boissel JP, Lee WR, Presnell SR, et al. (1993) Erythropoietin structure-function relationships. Mutant proteins that test a model of tertiary structure. J Biol Chem 268:15983-15993

Bonneau R, Baker D (2001) Ab initio protein structure prediction: progress and prospects. Annu Rev Biophys Biomol Struct 30:173-189

Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164—170

Braun W, Go N (1985) Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J Mol Biol 186:611-626

Brenner SE, Chothia C, Hubbard TJ (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 95:6073-6078

Brooks CL, ІП, Bruccoleri RE, Olafson BD, et al. (1983) CHARMM:A program for macromolecular energy minimization and dynamics calculations. J Comp Chem 4:187-217

Browne WJ, North ACT, Phillips DC, et al. (1969) A possible three-dimensional structure of bovine lactalbumin based on that of hen’s egg-white lysosyme. J Mol Biol 42:65-86

Bruccoleri RE, Karplus M (1987) Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137-168

Bruccoleri RE, Karplus M (1990) Conformational sampling using high-temperature molecular dynamics. Biopolymers 29:1847-1862

Bujnicki JM, Elofsson A, Fischer D, et al. (2001) LiveBench-T. continuous benchmarking of protein structure prediction servers. Protein Sci 10:352-362

Burley SK, Almo SC, Bonanno JB, et al. (1999) Structural genomics: beyond the human genome project. Nat Genet 23:151-157

Burley SK, Joachimiak A, Montelione GT, et al. (2008) Contributions to the NIH-NIGMS protein structure initiative from the PSI production centers. Structure 16:5-11

Bystroff C, Baker D (1998) Prediction of local structure in proteins using a library of sequence structure motifs. J Mol Biol 281:565-577

Chakravarty S, Sanchez R (2004) Systematic analysis of added-value in simple comparative models of protein structure. Structure 12:1461—1470

Chakravarty S, Wang L, Sanchez R (2005) Accuracy of structure-derived properties in simple comparative models of protein structures. Nucleic Acids Res 33:244-259

Chance MR, Bresnick AR, Burley SK, et al. (2002) Structural genomics: a pipeline for providing structures for the biologist. Protein Sci 11:723-738

Chinea G, Padron G, Hooft RW, et al. (1995) The use of position-specific rotamers in model building by homology. Proteins 23:415-421

Chivian D, Baker D (2006) Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res 34:el 12

Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826

Chothia C, Lesk AM (1987) Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 196:901-917

Chothia C, Lesk AM, Tramontano A, et al. (1989) Conformations of immunoglobulin hypervariable regions. Nature 342:877-883

Chothia C, Gough J, Vogel C, et al. (2003) Evolution of the protein repertoire. Science 300:1701-1703

Claessens М, Van Cutsem E, Lasters I, et al. (1989) Modelling the polypeptide backbone with ’spare parts’ from known protein structures. Protein Eng 2:335-345 /

Clore GM, Brunger AT, Karplus M, et al. (1986) Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination. A model study of crambin. J Mol Biol 191:523—551

Clore GM, Robien MA, Gronenbom AM (1993) Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J Mol Biol 231:82-102

Cohen FE, Kuntz ID: Tertiary structure prediction, in Prediction of protein structure and the principles of protein conformations. Edited by Fasman GD. New York, Plenum, 1989, pp. 647-705

Collura V, Higo J, Gamier J (1993) Modeling of protein loops by simulated annealing. Protein Sci 2:1502-1510

Contreras-Moreira B, Fitqohn PW, Offinan M, et al. (2003) Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins 53(Suppl 6): 424—429

Dalton JA, Jackson RM (2007) An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 23:1901—1908

Das B, Meirovitch H (2003) Solvation parameters for predicting the structure of surface loops in proteins: transferability and entropie effects. Proteins 51:470-483

Das R, Qian B, Raman S, et al. (2007) Structure prediction for CASP7 targets using extensive all atom refinement with Rosetta@home. Proteins 69(Suppl 8): 118-128

de Bakker PI, DePristo MA, Burke DF, et al. (2003) Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Bom solvation model. Proteins 51:21-40

Deane CM, Blundell TL (2001) CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 10:599-612

DePristo MA, de Bakker PI, Lovell SC, et al. (2003) Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 51:41—55

Dill KA, Chan HS (1997) From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19

Do CB, Mahabhashyam MS, Brudno M, et al. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 15:330-340

Du P, Andrec M, Levy RM (2003) Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng 16:407-414

Edgar RC, Batzoglou S (2006) Multiple sequence alignment. Curr Opin Struct Biol 16:368-373

Edgar RC, Sjolander К (2003) SATCHMO: sequence alignment and tree construction using hidden Markov models. Bioinformatics 19:1404—1411

Edgar RC, Sjolander К (2004) COACH: profile-profile alignment of protein families using hidden Maikov models. Bioinformatics 20:1309-1318

Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Method Enzymol 277:396-404

Eramian D, Shen MY, Devos D, et al. (2006) A composite score for predicting errors in protein structure models. Protein Sci 15:1653-1666

Espadaler J, Femandez-Fuentes N, Hermoso A, et al. (2004) ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res 32:D 185-188

Evers A, Gohlke H, Klebe G (2003) Ligand-supported homology modelling of protein binding sites using knowledge-based potentials. J Mol Biol 334:327-345

Eyrich VA, Marti-Renom MA, Przybylski D, et al. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 17:1242-1243

Faber HR, Matthews BW (1990) A mutant T4 lysozyme displays five different crystal conformations. Nature 348:263-266

Fasnacht M, Zhu J, Honig В (2007) Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci 16:1557-1568

Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376

Femandez-Fuentes N, Fiser A (2006) Saturating representation of loop conformational fragments in structure databanks. BMC Struct Biol 6:15

Femandez-Fuentes N, Oliva В, Fiser А (2006а) A supersecondaiy structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 34:2085-2097

Femandez-Fuentes N, Zhai J, Fiser A (2006b) ArchPRED: a template based loop structure prediction server. Nucleic Acids Res 34:W173-176

Femandez-Fuentes N, Madrid-Aliste CJ, Rai BK, et al. (2007a) M4T: a comparative protein structure modeling server. Nucleic Acids Res 35:W363-368

Femandez-Fuentes N, Rai BK, Madrid-Aliste CJ, et al. (2007b) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-stmcture alignments. Bioinformatics 23:2558-2565

Fidelis К, Stem PS, Bacon D, et al. (1994) Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 7:953-960

Fine RM, Wang H, Shenkin PS, et al. (1986) Predicting antibody hypervariable loop conformations. II: minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations. Proteins 1:342-362

Finkeistein AV, Reva BA (1991) A search for the most stable folds of protein chains. Nature 351:497-499

Fiser A (2004) Protein structure modeling in the proteomics era. Expert Rev Proteomics 1:97—110

Fiser A, Sali A (2003a) Modeller: generation and refinement of homology-based protein structure models. Method Enzymol 374:461-491

Fiser A, Sali A (2003b) ModLoop: automated modeling of loops in protein structures. Bioinformatics 19:2500-2501

Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein Sci 9:1753-1773

Fiser A, Feig M, Brooks CL, III, et al. (2002) Evolution and physics in comparative protein structure modeling. Acc Chem Res 35:413—421

Fiser A, Filipe SR, Tomasz A (2003) Cell wall branches, penicillin resistance and the secrets of the MurM protein. Trends Microbiol 11:547-553

Fogolari F, Tosatto SC (2005) Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation. Protein Sci 14:889-901

Forrest LR, Woolf ТВ (2003) Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions. Proteins 52:492- 509

Ginalski К (2006) Comparative modeling for protein structure prediction. Curr Opin Struct Biol 16:172-177

Ginalski K, Elofsson A, Fischer D, et al. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19:1015-1018

Grabarek Z (2006) Structural basis for diversity of the EF-hand calcium-binding proteins. J Mol Biol 359:509-525

Greene LH, Lewis TE, Addou S, et al. (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35:D291-297

Greer J (1981) Comparative model-building of the mammalian serine proteases. J Mol Biol 153:1027-1042

Greer J (1990) Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins 7:317-334

Guenther B, Onrust R, Sali A, et al. (1997) Crystal structure of the alpha-subunit of the clamp loader complex of E. coli DNA polymerase III. Cell 91:335-345

Han R, Leo-Macias A, Zerbino D, et al. (2008) An efficient conformational sampling method for homology modeling. Proteins 71:175-188

Havel TF, Snow ME (1991) A new method for building protein conformations from sequence alignments with homologues of known structure. J Mol Biol 217:1-7

Henikoff JQ Pietrokovski S, McCallum CM, et al. (2000) Blocks-based methods for detecting protein homology. Electrophoresis 21:1700-1706

Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919.

Holm L, Sander C (1991) Database algorithm for generating protein backbone and side-chain coordinates from a C alpha trace application to model building and detection of co-ordinate errors. J Mol Biol 218:183-194

Hooft RW, Vriend G, Sander C, et al. (1996) Errors in protein structures. Nature 381:272

Jacobson MP, Pincus DL, Rapp CS, et al. (2004) A hierarchical approach to all-atom protein loop prediction. Proteins 55:351—367

Jaroszewski L, Rychlewski L, Li Z, et al. (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 33:W284-288

Jauch R, Yeo HC, Kolatkar PR, et al. (2007) Assessment of CASP7 structure predictions for template free targets. Proteins 69(Suppl 8):57-67

Jennings AJ, Edge CM, Sternberg MJ (2001) An approach to improving multiple alignments of protein sequences using predicted secondary structure. Protein Eng 14:227-231

John B, Sali A (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 31:3982-3992

John B, Sali A (2004) Detection of homologous proteins by an intermediate sequence search. Protein Sci 13:54-62

Johnson LN, Lowe ED, Noble ME, et al. (1998) The Eleventh Datta Lecture. The structural basis for substrate recognition and control by protein kinases. FEBS Lett 430:1-11

Jones DT (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287:797-815

Jones TA, Thirup S (1986) Using known substructures in protein model building and crystallography. EMBO J 5:819-822

Karchin R, Cline M, Mandel-Gutfreund Y, et al. (2003) Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 51:504-514

Karplus K, Barrett C, Hughey R (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14:846-856

Karplus K, Katzman S, Shackleford G, et al. (2005) SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 61(Suppl 7): 135-142

Kihara D, Skolnick J (2003) The PDB is a covering set of small protein structures. J Mol Biol 334:793-802

Kiselar JG, Jantney PA, Almo SC, et al. (2003) Structural analysis of gelsolin using synchrotron protein footprinting. Mol Cell Proteomics 2:1120-1132

Koehl P, Delame M (1995) A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat Struct Biol 2:163-170

Kolinski A, Bujnicki JM (2005) Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 61(Suppl 7):84—90

Kolinski A, Betancourt MR, Kihara D, et al. (2001) Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 44:133-149

Kopp J, Schwede T (2006) The SWISS-MODEL Repository: new features and functionalities.Nucleic Acids Res 34:D315-318

Kopp J, Bordoli L, Battey JN, et al. (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins 69(Suppl 8):38-56

Krogh A, Brown M, Mian IS, et al. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol 235:1501-1531

Laskowski RA, Moss DS, Thornton JM (1993) Main-chain bond lengths and bond angles in protein structures. J Mol Biol 231:1049— 1067

Lesk AM (1995) NAD-binding domains of dehydrogenases. Curr Opin Struct Biol 5:775-783

Lesk AM, Chothia C (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136:225-270

Levitt M (1992) Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226:507-533

Luthy R, McLachlan AD, Eisenberg D (1991) Secondary structure-based profiles: use of structure conserving scoring tables in searching protein sequence databases for structural similarities. Proteins 10:229-239.

Manjasetty BA, Shi W, Zhan C, et al. (2007) A high-throughput approach to protein structure analysis. Genet Eng (NY) 28:105—128

Marti-Renom MA, Stuart AC, Fiser A, et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325

Marti-Renom MA, Madhusudhan MS, Fiser A, et al. (2002) Reliability of assessment of protein structure prediction methods. Structure(Camb) 10:435-440

Marti-Renom MA, Madhusudhan MS, Sali A (2004) Alignment of protein sequences by their profiles. Protein Sci 13:1071-1087

Melo F, Feytmans E (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267:207-222

Mezei M (1998) Chameleon sequences in the PDB. Protein Eng 11.411-414

Michalsky E, Goede A, Preissner R (2003) Loops In Proteins (LIP)-a comprehensive loop database for homology modelling. Protein Eng 16:979-985

Moretti S, Armougom F, Wallace IM, et al. (2007) The М-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res 35:W645-648

Moult J (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 15:285-289

Moult J, James MN (1986) An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1:146-163

Notredame C (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 3:e 123

Ohlendorf DH (1994) Accuracy of refined protein structures. Comparison of four independently refined models of human interleukin 1 beta. Acta Crystallogr D Biol Crystallogr D50:808-812

Oliva B, Bates PA, Querol E, et al. (1997) An automated classification of the structure of protein loops. J Mol Biol 266:814-830

Orr GA, Rao S, Swindell CS, et al. (1998) Photoaffinity labeling approach to map the Taxol- binding site on the microtubule. Method Enzymol 298:238-252

Pearson WR (2000) Flexible sequence similarity searching with the FASTA3 program package. Method Mol Biol 132:185-219

Pei J, Grishin NV (2007) PROM ALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 23:802-808

Pei J, Kim BH, Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 36:2295-2300

Peng HP, Yang AS (2007) Modeling protein loops with knowledge-based prediction of sequence structure alignment. Bioinformatics 23:2836-2842

Petrey D, Honig В (2005) Protein structure prediction: inroads to biology. Mol Cell 20:811-819

Petrey D, Xiang Z, Tang CL, et al. (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53(Suppl 6): 430-435

Pieper U, Eswar N, Davis FP, et al. (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34D291-295

Pillardy J, Czapiewski C, Li wo A, et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci USA 98:2329- 23233

Qian B, Ortiz AR, Baker D (2004) Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proc Natl Acad Sci USA 101:15346-15351

Rai BK, Fiser A (2006) Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling. Proteins 63:644-661

Rai BK, Madrid-Aliste CJ, Fajardo JE, et al. (2006) МММ: a sequence-to-structure alignment protocol. Bioinformatics 22:2691-2692

Sali A, Matsumoto R, McNeil HP, et al. (1993) Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan binding regions and protease-specific antigenic epitopes. J Biol Chem 268:9023-9034

Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369:248-251

Samudrala R, Moult J (1998) A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279:287-302

Sanchez R, Sali A (1997) Evaluation of comparative protein structure modeling by MODELLER-3. Proteins(Suppl l):50-58

Sanchez R, Sali A (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 95:13597-13602

Sangar V, Blankenberg DJ, Altman N, et al. (2007) Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8:294

Saraste M, Sibbald PR, Wittinghofer A (1990) The P-loop-a common motif in ATP- and GTP- binding proteins. Trends Biochem Sci 15:430-434

Sauder JM, Arthur JW, Dunbrack RL, Jr. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins 40:6-22

Schaffer AA, Aravind L, Madden TL, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29:2994-3005

Schwarzenbacher R, Godzik A, Jaroszewski L (2008) The JCSG MR pipeline: optimized alignments, multiple models and parallel searches. Acta Crystallogr D Biol Crystallogr 64:133-140

Sheng Y, Sali A, Herzog H, et al. (1996) Site-directed mutagenesis of recombinant human beta 2- glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity. J Immunol 157:3744-3751

Shenkin PS, Yarmush DL, Fine RM, et al. (1987) Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers 26:2053-2085

Shi J, Blundell TL, Mizuguchi К (2001) FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 310:243-257

Sibanda BL, Blundell TL, Thornton JM (1989) Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206:759-777

Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883

Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355—362

Sippl MJ (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229-235

Soto CS, Fasnacht M, Zhu J, et al. (2008) Loop modeling: Sampling, filtering, and scoring. Proteins 70:834—843

Srinivasan N, Blundell TL (1993) An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng 6:501-512

Summa CM, Levitt M (2007) Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 104:3177-3182

Sutcliffe MJ, Haneef I, Carney D, et al. (1987) Knowledge based modelling of homologous proteins, Part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1:377-384

Sutcliffe MJ, Dobson CM, Oswald RE (1992) Solution structure of neuronal bungarotoxin determined by two-dimensional NMR spectroscopy: calculation of tertiary structure using systematic homologous model building, dynamical simulated annealing, and restrained molecular dynamics. Biochemistry 31:2962-2970

Tainer JA, Thayer MM, Cunningham RP (1995) DNA repair proteins. Curr Opin Struct Biol 5:20-26

Taylor WR, Hatrick К (1994) Compensating changes in protein multiple sequence alignments. Protein Eng 7:341-348

Terashi Q Takeda-Shitaka M, Kanou K, et al. (2007) Fams-ace: a combined method to select the best model after remodeling all server models. Proteins 69(Suppl 8):98-107 Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143

Todd AE, Orengo CA, Thornton JM (2002) Plasticity of enzyme active sites. Trends Biochem Sci 27:419-426

Topf M, Lasker К, Webb В, et al. (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16:295-307

Topham CM, McLeod A, Eisenmenger F, et al. (1993) Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol 229:194-220

Unger R, Harel D, Wherland S, et al. (1989) A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 5:355-373

Vakser LA (1995) Protein docking for low-resolution structures. Protein Eng 8:371-377

van Gelder CW, Leusen FJ, Leunissen JA, et al. (1994) A molecular dynamics approach for the generation of complete protein structures from limited coordinate data. Proteins 18:174—185

van Vlijmen HW, Karplus M (1997) PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 267:975-1001

Venclovas C, Margelevicius M (2005) Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins 61:99-105.

Venter JC, Remington K, Heidelberg JF, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74

Vernal J, Fiser A, Sali A, et al. (2002) Probing the specificity of a trypanosomal aromatic alphahydroxy acid dehydrogenase by site-directed mutagenesis. Biochem Biophys Res Commun 293:633-639

Vitkup D, Melamud E, Moult J, et al. (2001) Completeness in structural genomics. Nat Struct Biol 8:559-566

Wallner B, Elofsson A (2005a) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21:4248—4254

Wallner B, Elofsson A (2005b) All are not equal: a benchmark of different homology modeling programs. Protein Sci 14:1315-1327

Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Peons and ProQ. Proteins 69(Suppl 8): 184-193

Wallner B, Larsson P, Elofsson A (2007) Pcons.net: protein structure prediction meta server. Nucleic Acids Res 35:W369-374

Wlodawer A, Miller М, Jaskólski М, et al. (1989) Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 245:616-621

Wu CH, Apweiler R, Bairoch A, et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187-191

Wu G, Fiser A, ter Kuile B, et al. (1999) Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proc Natl Acad Sci USA 96:6285-6290

Wu G, McArthur AQ Fiser A, et al. (2000) Core histones of the amitochondriate protist, Giardia lamblia. Mol Biol Evol 17:1156-1163

Xiang Z, Soto CS, Honig В (2002) Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. Proc Natl Acad Sсi USA 99:7432-7437

Xiao H, Verdier-Pinard P, Femandez-Fuentes N, et al. (2006) Insights into the mechanism of microtubule stabilization by Taxol. Proc Natl Acad Sci USA 103:10166-10173

Xu J, Jiao F, Yu L (2007) Protein structure prediction using threading. Methods Mol Biol 413:91-122

Xu LZ, Sanchez R, Sali A, et al. (1996) Ligand specificity of brain lipid-binding protein. J Biol Chem 271:24711-24719

Yooseph S, Sutton G, Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5:e16

Zhang C, Liu S, Zhou Y (2004) Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci 13:391-399

Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 69(Suppl 8): 108-117

Zheng Q, Rosenfeld R, Vajda S, et al. (1993) Determining protein loop conformation using scaling-relaxation techniques. Protein Sci 2:1242-1248

Zhou H, Pandit SB, Lee SY, et al. (2007) Analysis of TASSER-based CASP7 protein structure prediction results. Proteins 69(Suppl 8):90-97



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