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

Предсказание структуры белков ab initio
Литература

Bairoch А, Apweiler R, Wu CH, et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res 33(Database issue):D154-159

Berendsen HJC, Postma JPM, van Gunsteren WF, et al. (1981) Interaction models for water in relation to protein hydration. Intermolecular forces. Reidel, Dordrecht, The Netherlands Berg BA, Neuhaus T (1992) Multicanonical ensemble: a new approach to simulate first-order phase transitions. Phys Rev Lett 68(1):9—12

Berman HM, Westbrook J, Feng Z, et al. (2000) The protein data bank. Nucleic Acids Res 28(l):235-242

Веrrеrа M, Molinari H, Fogolari F (2003) Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4:8 Bowie JU, Eisenberg D (1994) An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 91(10)4436-4440

Bradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309(5742): 1868-1871

Brooks BR, Broccoleri RE, Olafson BD, et al. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2): 187-217 Bryant SH, Lawrence CE (1993) An empirical energy flmction for threading protein sequence through the folding motif. Proteins 16(1):92—112

Case DA, Pearlman DA, Caldwell JA, et al. (1997) AMBER 5.0, University of California, San Francisco, CA.

Chen J, Brooks CL (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67(4):922-930

Cheng J, Baldi P (2006) A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22(12): 1456-1463

Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2(9): 1511-1519

Cornell WD, Cieplak P, Bayly Cl, et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 117:5179-5197

Das R, Qian B, Raman S, et al. (2007) Structure prediction for CASP7 targets using extensive allatom refinement with Rosetta@home. Proteins 69(S8):118-128

Dominy BN, Brooks CL (2002) Identifying native-like protein structures using physics-based potentials. J Comput Chem 23(1): 147-160

Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282(5389):740-744

Eisenberg D, Luthy R, Bowie JU (1997) VEREFY3D: assessment of protein models with threedimensional profiles. Method Enzymol 277:396-404

Fan H, Mark AE (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sei 13(1):211-220

Feig M, Brooks CL (2002) Evaluating CASP4 predictions with physical energy functions. Proteins 49(2):232-245

Felts AK, Gallicchio E, Wallqvist A, et al. (2002) Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the Surface Generalized Bom solvent model. Proteins 48(2)404—422

Fischer D (2006) Servers for protein structure prediction. Curr Opin Struct Biol 16(2): 178-182

Fujitsuka Y, Chikenji G, Takada S (2006) SimFold energy flmction for de novo protein structure prediction: consensus with Rosetta. Proteins 62(2):381-398

Ginalski K, Elofsson A, Fischer D, et al. (2003a) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19(8): 1015-1018

Ginalski K, Pas J, Wyrwicz LS, et al. (2003b) ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res 31(13):3804-3807

Hagler A, Euler E, Lifson S (1974) Energy functions for peptides and proteins L Derivation of a consistent force field including the hydrogen bond from amide crystals. J Am Chem Soc 96:5319-5327

Helles G (2008) A comparative study of the reported performance of ab initio protein structure prediction algorithms. J R Soc Interface 5(21):387—396

Hendlich M, Lackner P, Weitckus S, et al. (1990) Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol 216(1): 167-180

Hsieh MJ, Luo R (2004) Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins 56(3):475-486

Im W, Lee MS, Brooks CL (2003) Generalized bom model with a simple smoothing function. J Comput Chem 24(14): 1691-1702

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

Jonassen I, Klose D, Taylor WR (2006) Protein model refinement using structural fragment tessellation. Comput Biol Chem 30(5):360-366

Jones DT (1999) GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287(4):797-815

Jorgensen WL, Tirado-Rives J (1988) The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J Am Chem Soc (110): 1657-1666

Jorgensen WL, Chandrasekhar J, Madura JD, et al. (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935

Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS All-Atom Force Field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236

Kaminski GA, Friesner RA, Tirado-Rives J, et al. (2001) Evaluation and Reparametrization of the OPLS-AA Force Field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem В 105:6474-6487

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

Kihara D, Lu H, Kolinski A, et al. (2001) TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 98(18): 10125— 10130

Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science 220(4598):671-680

Klepeis JL, Floudas CA (2003) ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J 85(4):2119—2146

Klepeis JL, Wei Y, Hecht MH, et al. (2005) Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 58(3):560-570

Kocher JP, Rooman MJ, Wodak SJ (1994) Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235(5): 1598—1613

Lazaridis T, Karplus M (1999a) Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 288(3):477—487

Lazaridis T, Karplus M (1999b) Effective energy function for proteins in solution. Proteins 35(2): 133-152

Lee J (1993) New Monte Carlo algorithm: entropie sampling. Phys Rev Lett 71 (2):211-214

Lee J, Scheraga HA, Rackovsky S (1998) Conformational analysis of the 20-residue membranebound portion of melittin by conformational space annealing. Biopolymers 46(2): 103-116

Lee J, Kim SY, Joo K, et al. (2004) Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing. Proteins 56(4):704-714

Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized bom solvent model. Proteins 55(3):620-634

Lee MR, Tsai J, Baker D, et al. (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313(2):417-430

Levitt M, Hirshberg M, Sharon R, et al. (1995) Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution. Comput Phys Commun 91 (1—3):215—231

Li Z, Scheraga HA (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 84(19):6611-6615

Lindahl E, Hess B, van der Spoel D (2001) GROM ACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306-317

Liwo A, Pincus MR, Wawak RJ, et al. (1993) Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment. Protein Sei 2(10): 1697- 1714

Liwo A, Lee J, Ripoll DR, et al. (1999) Protein structure prediction by global optimization of a potential energy function. Proc Natl Acad Sci USA 96(10):5482-5485

Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci USA 102(7):2362-2367

Lu H, Skolnick J (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44(3):223-232

Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356(6364):83-85

MacKerell Jr. AD, Bashford D, Bellott M, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem В 102 (18):3586—3616

McGuffin LJ (2007) Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics 8:345

Melo F, Sanchez R, Sali A (2002) Statistical potentials for fold assessment. Protein Sci 11 (2):430—448

Moult J, Fidelis К, Zemla A, et al. (2001) Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins(Suppl 5):2-7

Nemethy G, Gibson KD, Palmer KA, et al. (1992) Energy parameters in polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem В 96: 6472-6484

Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105(5): 1902 -1921

Nilges M, Bronger AT (1991) Automated modeling of coiled coils: application to the GCN4 dimerization region. Protein Eng 4(6):649-659

Oldziej S, Czapiewski C, Liwo A, et al. (2005) Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci USA 102(21 ):7547-7552

Park B, Levitt M (1996) Energy functions that discriminate X-ray and near native folds from well constructed decoys. J Mol Biol 258(2):367-392

Petrey D, Honig В (2000) Free energy determinants of tertiary structure and the evaluation of protein models. Protein Sci 9(11):2181-2191

Pettitt CS, McGuffin LJ, Jones DT (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21 (17):3509—3515

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

Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275(5):895-916

Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15(11):2507—2524

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(1):243—257

Shortle D, Simons KT, Baker D (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95(19): 111 58—11162

Simons KT, Kooperberg C, Huang E, et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268(1):209-225

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(4):859—883

Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17(4):355—362

Skolnick J (2006) In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 16(2): 166-171

Skolnick J, Jaroszewski L, Kolinski A, et al. (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Science 6:676-688 Skolnick J, Zhang Y, Arakaki AK, et al. (2003) TOUCHSTONE: a unified approach to protein structure prediction. Proteins 53(Suppl 6):469-479

Skolnick J, Kihara D, Zhang Y (2004) Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Protein 56:502-518

Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-960

Sorin EJ, Pande VS (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys J 88(4):2472-2493

Summa CM, Levitt M (2007) Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 104(9):3177-3182

Taylor WR, Bartlett GJ, Chelliah V, et al. (2008) Prediction of protein structure from ideal forms. Proteins 70(4): 1610-1619

Thomas PD, Dill KA (1996) Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 257(2):457-469

Tosatto SC (2005) The victor/FRST function for model quality estimation. J Comput Biol 12(10): 1316—1327

Tsai J, Bonneau R, Morozov AV, et al. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53(l):76-87

van Gunsteren WF, Billeter SR, Eising AA, et al. (1996) Biomolecular simulation: the GROMOS96 manual and user guide. VDF Hochschulverlag AG an der ETH, Zurich. Vieth M, Kolinski A, Brooks CL, et al. (1994) Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol 237(4):361-367

Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12(5): 1073—1086

Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Peons and ProQ. Proteins 69(S8): 184-193

Wang JM, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? JComput Chem 21 (12): 1049-1074

Wang K, Fain B, Levit M, et al. (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol 4(8)

Weiner SJ, Kollman PA, Case DA, et al. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106: 765-784

Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue): W407- 410

Wróblewska L, Skolnick J (2007) Can a physics-based, all-atom potential find a protein’s native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem 28(12):2059-2066

Wu S, Zhang Y (2007) LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 35(10):3375-3382

Wu S, Zhang Y (2008) MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72(2):547-556

Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17

Zagrovic B, Snow CD, Shirts MR, et al. (2002) Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol 323(5):927-937

Zhang C, Kim SH (2000) Environment-dependent residue contact energies for proteins. Proc Natl Acad Sci USA 97(6):2550-2555

Zhang C, Liu S, Zhou H, et al. (2004) An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 13(2):400-411

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

Zhang Y (2008) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18(3):342-348

Zhang Y, Skolnick J (2004a) Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A 101:7594-7599

Zhang Y, Skolnick J (2004b) Scoring function for automated assessment of protein structure template quality. Proteins 57:702-710

Zhang Y, Skolnick J (2004c) SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 25(6):865-871

Zhang Y, Skolnick J (2005a) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 102:1029-1034

Zhang Y, Skolnick J (2005b) TM-align: a protein structure alignment algorithm based on the TMscore. Nucleic Acids Res 33(7):2302-2309

Zhang Y, Kihara D, Skolnick J (2002) Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 48(2): 192-201

Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85(2): 1145-1164

Zhang Y, Hubner I, Arakaki A, et al. (2006) On the origin and completeness of highly likely single domain protein structures. Proc Natl Acad Sci USA 103:2605-2610

Zhou H, Skolnick J (2007) Ab initio protein structure prediction using chunk-TASSER. Biophys J 93(5): 1510—1518

Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure derived potentials of mean force for structure selection and stability prediction. Protein Sci 11(11):2714-2726

Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58(2):321-328