-
1
-
-
33644874606
-
The SWISS-MODEL Repository: New features and functionalities
-
Kopp J, Schwede T. (2006) The SWISS-MODEL Repository: new features and functionalities. Nucl Acids Res 34: D315-D318.
-
(2006)
Nucl Acids Res
, vol.34
, pp. D315-D318
-
-
Kopp, J.1
Schwede, T.2
-
2
-
-
33644874394
-
MODBASE: A database of annotated comparative protein structure models and associated resources
-
Pieper U, Eswar N, Davis FP, et al. (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucl Acids Res 34: D291-D295.
-
(2006)
Nucl Acids Res
, vol.34
, pp. D291-D295
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
-
3
-
-
33644877685
-
The PMDB Protein Model Database
-
Castrignano T, De Meo PD, Cozzetto D, Talamo IG, Tramontano A. (2006) The PMDB Protein Model Database. Nucl Acids Res 34: D306-D309.
-
(2006)
Nucl Acids Res
, vol.34
, pp. D306-D309
-
-
Castrignano, T.1
De Meo, P.D.2
Cozzetto, D.3
Talamo, I.G.4
Tramontano, A.5
-
4
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. (2001) Protein structure prediction and structural genomics. Science 294: 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
6
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
Miyazawa S, Jernigan RL. (1996) Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256: 623-644.
-
(1996)
J Mol Biol
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
7
-
-
0032613428
-
Sustained performance of knowledge-based potentials in fold recognition
-
Domingues FS, Koppensteiner WA, Jaritz M, et al. (1999) Sustained performance of knowledge-based potentials in fold recognition. Proteins (3): 112-120.
-
(1999)
Proteins
, Issue.3
, pp. 112-120
-
-
Domingues, F.S.1
Koppensteiner, W.A.2
Jaritz, M.3
-
8
-
-
0036145846
-
Statistical potentials for fold assessment
-
Melo F, Sanchez R, Sali A. (2002) Statistical potentials for fold assessment. Protein Sci 11: 430-448.
-
(2002)
Protein Sci
, vol.11
, pp. 430-448
-
-
Melo, F.1
Sanchez, R.2
Sali, A.3
-
9
-
-
0038634975
-
Improvement of the GenTHREADER method for genomic fold recognition
-
McGuffin LJ, Jones DT. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
-
(2003)
Bioinformatics
, vol.19
, pp. 874-881
-
-
McGuffin, L.J.1
Jones, D.T.2
-
10
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T, Karplus M. (1999) Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 288:477-487.
-
(1999)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
11
-
-
0034560338
-
Discrimination of near-native protein structures from misfolded models by empirical free energy functions
-
Gatchell DW, Dennis S, Vajda S. (2000) Discrimination of near-native protein structures from misfolded models by empirical free energy functions. Proteins 41: 518-534.
-
(2000)
Proteins
, vol.41
, pp. 518-534
-
-
Gatchell, D.W.1
Dennis, S.2
Vajda, S.3
-
12
-
-
0035186285
-
Free energies of protein decoys provide insight into determinants of protein stability
-
Vorobjev YN, Hermans J. (2001) Free energies of protein decoys provide insight into determinants of protein stability. Protein Sci 10: 2498-2506.
-
(2001)
Protein Sci
, vol.10
, pp. 2498-2506
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
13
-
-
0037439987
-
MOPED: Method for optimizing physical energy parameters using decoys
-
Seok C, Rosen JB, Chodera JD, Dill KA. (2003) MOPED: method for optimizing physical energy parameters using decoys. J Comput Chem 24: 89-97.
-
(2003)
J Comput Chem
, vol.24
, pp. 89-97
-
-
Seok, C.1
Rosen, J.B.2
Chodera, J.D.3
Dill, K.A.4
-
14
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 53: 76-87.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Morozov, A.V.3
Kuhlman, B.4
Rohl, C.A.5
Baker, D.6
-
15
-
-
0042921442
-
How well can we predict native contacts in proteins based on decoy structures and their energies?
-
Zhu J, Zhu Q, Shi Y, Liu H. (2003) How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins 52: 598-608.
-
(2003)
Proteins
, vol.52
, pp. 598-608
-
-
Zhu, J.1
Zhu, Q.2
Shi, Y.3
Liu, H.4
-
16
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J. (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44: 223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
17
-
-
34547298869
-
Can a physics-based, all-atom potential find a protein’s native structure among misfolded structures? I. Large scale AMBER benchmarking
-
Wroblewska 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: 2059-2066.
-
(2007)
J Comput Chem
, vol.28
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
18
-
-
0036681394
-
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 Born solvent model
-
Felts AK, Gallicchio E, Wallqvist A, Levy RM. (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 Born solvent model. Proteins 48: 404-422.
-
(2002)
Proteins
, vol.48
, pp. 404-422
-
-
Felts, A.K.1
Gallicchio, E.2
Wallqvist, A.3
Levy, R.M.4
-
19
-
-
0037079585
-
Identifying native-like protein structures using physics-based potentials
-
Dominy BN, Brooks CL. (2002) Identifying native-like protein structures using physics-based potentials. J Comput Chem 23: 147-160.
-
(2002)
J Comput Chem
, vol.23
, pp. 147-160
-
-
Dominy, B.N.1
Brooks, C.L.2
-
20
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle D, Simons KT, Baker D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95:11158-11162.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
21
-
-
0037406141
-
Can correct protein models be identified?
-
Wallner B, Elofsson A. (2003) Can correct protein models be identified? Protein Sci 12: 1073-1086.
-
(2003)
Protein Sci
, vol.12
, pp. 1073-1086
-
-
Wallner, B.1
Elofsson, A.2
-
22
-
-
34548809141
-
A coarse-grained protein force field for folding and structure prediction
-
Maupetit J, Tuffery P, Derreumaux P. (2007) A coarse-grained protein force field for folding and structure prediction. Proteins 69(2): 394-408.
-
(2007)
Proteins
, vol.69
, Issue.2
, pp. 394-408
-
-
Maupetit, J.1
Tuffery, P.2
Derreumaux, P.3
-
23
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
-
Park B, Levitt M. (1996) Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 258: 367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
24
-
-
34447502155
-
Form finds function
-
Allen KN. (2007) Form finds function. Nat Chem Biol 3: 452-453.
-
(2007)
Nat Chem Biol
, vol.3
, pp. 452-453
-
-
Allen, K.N.1
-
26
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, et al. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
-
27
-
-
0038650794
-
Protocol for MM/PBSA molecular dynamics simulations of proteins
-
Fogolari F, Brigo A, Molinari H. (2003) Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys J 85: 159-166.
-
(2003)
Biophys J
, vol.85
, pp. 159-166
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
28
-
-
11244289541
-
Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme
-
Soares TA, Daura X, Oostenbrink C, Smith LJ, van Gunsteren WF. (2004) Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme. J Biomol NMR 30: 407-422.
-
(2004)
J Biomol NMR
, vol.30
, pp. 407-422
-
-
Soares, T.A.1
Daura, X.2
Oostenbrink, C.3
Smith, L.J.4
van Gunsteren, W.F.5
-
29
-
-
2442480826
-
Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
-
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 born solvent model. Proteins 55: 620-634.
-
(2004)
Proteins
, vol.55
, pp. 620-634
-
-
Lee, M.C.1
Duan, Y.2
-
30
-
-
3142680776
-
Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction
-
Hsieh MJ, Luo R. (2004) Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction. Proteins 56: 475-486.
-
(2004)
Proteins
, vol.56
, pp. 475-486
-
-
Hsieh, M.J.1
Luo, R.2
-
31
-
-
0035914481
-
Molecular dynamics in the endgame of protein structure prediction
-
Lee MR, Tsai J, Baker D, Kollman PA. (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313: 417-430.
-
(2001)
J Mol Biol
, vol.313
, pp. 417-430
-
-
Lee, M.R.1
Tsai, J.2
Baker, D.3
Kollman, P.A.4
-
32
-
-
15244349255
-
Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
-
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.
-
(2005)
Protein Sci
, vol.14
, pp. 889-901
-
-
Fogolari, F.1
Tosatto, S.C.2
-
33
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
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.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
34
-
-
0037188507
-
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
-
Xiang Z, Soto CS, Honig B. (2002) Evaluating conformational free energies:the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 99: 7432-7437.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7432-7437
-
-
Xiang, Z.1
Soto, C.S.2
Honig, B.3
-
35
-
-
0016885150
-
Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins
-
Tanaka S, Scheraga HA. (1976) Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins. Macromolecules 9: 142-159.
-
(1976)
Macromolecules
, vol.9
, pp. 142-159
-
-
Tanaka, S.1
Scheraga, H.A.2
-
36
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
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.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
37
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation
-
Miyazawa S, Jernigan RL. (1985) Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules 18: 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
38
-
-
0017309766
-
Structural patterns in globular proteins
-
Levitt M, Chothia C. (1976) Structural patterns in globular proteins. Nature 261: 552-558.
-
(1976)
Nature
, vol.261
, pp. 552-558
-
-
Levitt, M.1
Chothia, C.2
-
39
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D, McLachlan AD. (1986) Solvation energy in protein folding and binding. Nature 319: 199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
40
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
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.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
41
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
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: 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
42
-
-
0027650879
-
Boltzmann’s principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
-
Sippl MJ. (1993) Boltzmann’s principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 7: 473-501.
-
(1993)
J Comput Aided Mol Des
, vol.7
, pp. 473-501
-
-
Sippl, M.J.1
-
43
-
-
0032540222
-
Assessing protein structures with a non-local atomic interaction energy
-
Melo F, Feytmans E. (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277: 1141-1152.
-
(1998)
J Mol Biol
, vol.277
, pp. 1141-1152
-
-
Melo, F.1
Feytmans, E.2
-
44
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
Shen MY, Sali A. (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15: 2507-2524.
-
(2006)
Protein Sci
, vol.15
, pp. 2507-2524
-
-
Shen, M.Y.1
Sali, A.2
-
45
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
46
-
-
0028801308
-
Why do protein architectures have Boltzmann-like statistics?
-
Finkelstein AV, Badretdinov A, Gutin AM. (1995) Why do protein architectures have Boltzmann-like statistics? Proteins 23: 142-150.
-
(1995)
Proteins
, vol.23
, pp. 142-150
-
-
Finkelstein, A.V.1
Badretdinov, A.2
Gutin, A.M.3
-
47
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas PD, Dill KA. (1996) Statistical potentials extracted from protein structures:how accurate are they? J Mol Biol 257: 457-469.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
48
-
-
0029563695
-
Are database-derived potentials valid for scoring both forward and inverted protein folding?
-
Rooman MJ, Wodak SJ. (1995) Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 8: 849-858.
-
(1995)
Protein Eng
, vol.8
, pp. 849-858
-
-
Rooman, M.J.1
Wodak, S.J.2
-
49
-
-
0031582083
-
Novel knowledge-based mean force potential at atomic level
-
Melo F, Feytmans E. (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267: 207-222.
-
(1997)
J Mol Biol
, vol.267
, pp. 207-222
-
-
Melo, F.1
Feytmans, E.2
-
50
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones DT, Taylor WR, Thornton JM. (1992) A new approach to protein fold recognition. Nature 358: 86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
51
-
-
2942694535
-
The dependence of all-atom statistical potentials on structural training database
-
Zhang C, Liu S, Zhou H, Zhou Y. (2004) The dependence of all-atom statistical potentials on structural training database. Biophys J 86: 3349-3358.
-
(2004)
Biophys J
, vol.86
, pp. 3349-3358
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
53
-
-
33646011728
-
In quest of an empirical potential for protein structure prediction
-
Skolnick J. (2006) In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 16: 166-171.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 166-171
-
-
Skolnick, J.1
-
54
-
-
0029000696
-
Knowledge-based potentials for proteins
-
Sippl MJ. (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol 5: 229-235.
-
(1995)
Curr Opin Struct Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.J.1
-
55
-
-
24344479166
-
Atomically detailed potentials to recognize native and approximate protein structures
-
Qiu J, Elber R. (2005) Atomically detailed potentials to recognize native and approximate protein structures. Proteins 61: 44-55.
-
(2005)
Proteins
, vol.61
, pp. 44-55
-
-
Qiu, J.1
Elber, R.2
-
56
-
-
1642534609
-
An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
-
Zhang C, Liu S, Zhou H, Zhou Y. (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: 400-411.
-
(2004)
Protein Sci
, vol.13
, pp. 400-411
-
-
Zhang, C.1
Liu, S.2
Zhou, H.3
Zhou, Y.4
-
57
-
-
1842454935
-
Orientational potentials extracted from protein structures improve native fold recognition
-
Buchete NV, Straub JE, Thirumalai D. (2004) Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci 13:862-874.
-
(2004)
Protein Sci
, vol.13
, pp. 862-874
-
-
Buchete, N.V.1
Straub, J.E.2
Thirumalai, D.3
-
58
-
-
34249778085
-
TAP score: Torsion angle propensity normalization applied to local protein structure evaluation
-
Tosatto SC, Battistutta R. (2007) TAP score: Torsion angle propensity normalization applied to local protein structure evaluation. BMC Bioinform 8: 155.
-
(2007)
BMC Bioinform
, vol.8
, pp. 155
-
-
Tosatto, S.C.1
Battistutta, R.2
-
59
-
-
4344697167
-
Local propensities and statistical potentials of backbone dihedral angles in proteins
-
Betancourt MR, Skolnick J. (2004) Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol 342: 635-649.
-
(2004)
J Mol Biol
, vol.342
, pp. 635-649
-
-
Betancourt, M.R.1
Skolnick, J.2
-
60
-
-
84969139241
-
QMEAN: A comprehensive scoring function for model quality assessment
-
press
-
Benkert P, Tosatto SCE, Schomburg D. (2007) QMEAN: a comprehensive scoring function for model quality assessment. Proteins, in press.
-
(2007)
Proteins
-
-
Benkert, P.1
Tosatto, S.C.E.2
Schomburg, D.3
-
61
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley P, Misura KM, Baker D. (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309: 1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.2
Baker, D.3
-
62
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures in CASP6
-
Zhang Y, Arakaki AK, Skolnick J. (2005) TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61(7): 91-98.
-
(2005)
Proteins
, vol.61
, Issue.7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
63
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins 57: 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
64
-
-
33745726716
-
A composite score for predicting errors in protein structure models
-
Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. (2006) A composite score for predicting errors in protein structure models. Protein Sci 15:1653-1666.
-
(2006)
Protein Sci
, vol.15
, pp. 1653-1666
-
-
Eramian, D.1
Shen, M.Y.2
Devos, D.3
Melo, F.4
Sali, A.5
Marti-Renom, M.A.6
-
65
-
-
0242299169
-
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
-
Wallner B, Fang H, Elofsson A. (2003) Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins 53(6): 534-541.
-
(2003)
Proteins
, vol.53
, Issue.6
, pp. 534-541
-
-
Wallner, B.1
Fang, H.2
Elofsson, A.3
-
66
-
-
11144241105
-
LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
-
Rychlewski L, Fischer D. (2005) LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction. Protein Sci 14: 240-245.
-
(2005)
Protein Sci
, vol.14
, pp. 240-245
-
-
Rychlewski, L.1
Fischer, D.2
-
67
-
-
30344475200
-
Progress over the first decade of CASP experiments
-
Kryshtafovych A, Venclovas C, Fidelis K, Moult J. (2005) Progress over the first decade of CASP experiments. Proteins 61(7): 225-236.
-
(2005)
Proteins
, vol.61
, Issue.7
, pp. 225-236
-
-
Kryshtafovych, A.1
Venclovas, C.2
Fidelis, K.3
Moult, J.4
-
68
-
-
4544355522
-
Improved protein structure selection using decoy-dependent discriminatory functions
-
Wang K, Fain B, Levitt M, Samudrala R. (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol 4: 8.
-
(2004)
BMC Struct Biol
, vol.4
, pp. 8
-
-
Wang, K.1
Fain, B.2
Levitt, M.3
Samudrala, R.4
-
69
-
-
0035703089
-
Rosetta in CASP4: Progress in ab initio protein structure prediction
-
Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. (2001) Rosetta in CASP4: Progress in ab initio protein structure prediction. Proteins (5): 119-126.
-
(2001)
Proteins
, Issue.5
, pp. 119-126
-
-
Bonneau, R.1
Tsai, J.2
Ruczinski, I.3
Chivian, D.4
Rohl, C.5
Strauss, C.E.6
Baker, D.7
-
70
-
-
1942519275
-
SPICKER: A clustering approach to identify nearnative protein folds
-
Zhang Y, Skolnick J. (2004) SPICKER: a clustering approach to identify nearnative protein folds. J Comput Chem 25: 865-871.
-
(2004)
J Comput Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
72
-
-
0033853177
-
Decoys "R" Us: A database of incorrect conformations to improve protein structure prediction
-
Samudrala R, Levitt M. (2000) Decoys "R" Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9: 1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
73
-
-
0037375742
-
Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
-
DePristo MA, de Bakker PI, Lovell SC, Blundell TL. (2003) Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 51: 41-55.
-
(2003)
Proteins
, vol.51
, pp. 41-55
-
-
DePristo, M.A.1
de Bakker, P.I.2
Lovell, S.C.3
Blundell, T.L.4
-
74
-
-
33746271105
-
Biomolecular modeling:Goals, problems, perspectives
-
van Gunsteren WF, Bakowies D, Baron R, et al. (2006) Biomolecular modeling:Goals, problems, perspectives. Angew Chem Int Ed Engl 45: 4064-4092.
-
(2006)
Angew Chem Int Ed Engl
, vol.45
, pp. 4064-4092
-
-
van Gunsteren, W.F.1
Bakowies, D.2
Baron, R.3
-
75
-
-
0029948769
-
Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure
-
Bowie JU, Zhang K, Wilmanns M, Eisenberg D. (1996) Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure. Meth Enzymol 266: 598-616.
-
(1996)
Meth Enzymol
, vol.266
, pp. 598-616
-
-
Bowie, J.U.1
Zhang, K.2
Wilmanns, M.3
Eisenberg, D.4
-
76
-
-
28144448406
-
The victor/FRST function for model quality estimation
-
Tosatto SC. (2005) The victor/FRST function for model quality estimation. J Comput Biol 12: 1316-1327.
-
(2005)
J Comput Biol
, vol.12
, pp. 1316-1327
-
-
Tosatto, S.C.1
-
77
-
-
0030624472
-
ANOLEA: A www server to assess protein structures
-
Melo F, Devos D, Depiereux E, Feytmans E. (1997) ANOLEA: a www server to assess protein structures. Ismb 5: 187-190.
-
(1997)
Ismb
, vol.5
, pp. 187-190
-
-
Melo, F.1
Devos, D.2
Depiereux, E.3
Feytmans, E.4
-
78
-
-
34547566446
-
ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Wiederstein M, Sippl MJ. (2007) ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucl Acids Res 35: W407-410.
-
(2007)
Nucl Acids Res
, vol.35
, pp. W407-W410
-
-
Wiederstein, M.1
Sippl, M.J.2
-
79
-
-
4043052866
-
Accurate prediction of solvent accessibility using neural networks-based regression
-
Adamczak R, Porollo A, Meller J. (2004) Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 56: 753-767.
-
(2004)
Proteins
, vol.56
, pp. 753-767
-
-
Adamczak, R.1
Porollo, A.2
Meller, J.3
-
80
-
-
33645228775
-
A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring
-
Sims GE, Kim SH. (2006) A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring. Proc Natl Acad Sci USA 103: 4428-4432.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 4428-4432
-
-
Sims, G.E.1
Kim, S.H.2
|