-
1
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
2
-
-
38549164691
-
GenBank
-
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2008; 36: D25-D30.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
3
-
-
0034060287
-
Structural genomics and its importance for gene function analysis
-
Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000; 18: 283-287.
-
(2000)
Nat Biotechnol
, vol.18
, pp. 283-287
-
-
Skolnick, J.1
Fetrow, J.S.2
Kolinski, A.3
-
4
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D. Protein structure prediction and structural genomics. Science 2001; 294: 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
-
5
-
-
12844260161
-
Comparative protein structure modeling and its applications to drug discovery
-
In: Overington J, editor. Annual Reports in Medicinal Chemistry, London: Inpharmatica
-
Jacobson M, Sali A. Comparative protein structure modeling and its applications to drug discovery. In: Overington J, editor. Annual Reports in Medicinal Chemistry, Vol. 39. London: Inpharmatica; 2004. pp 259-276.
-
(2004)
, vol.39
, pp. 259-276
-
-
Jacobson, M.1
Sali, A.2
-
7
-
-
66149123302
-
Protein structure prediction by pro-Sp3-TASSER
-
Zhou H, Skolnick J. Protein structure prediction by pro-Sp3-TASSER. Biophys J 2009; 96: 2119-2127.
-
(2009)
Biophys J
, vol.96
, pp. 2119-2127
-
-
Zhou, H.1
Skolnick, J.2
-
8
-
-
77954065271
-
I-TASSER: a unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010; 5: 725-738.
-
(2010)
Nat Protoc
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
9
-
-
29144526714
-
Protein structure prediction: inroads to biology
-
Petrey, D. andHonig, B. Protein structure prediction: inroads to biology. Mol Cell 2005; 20: 811-819.
-
(2005)
Mol Cell
, vol.20
, pp. 811-819
-
-
Petrey, D.1
Honig, B.2
-
10
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008; 18: 342-348.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 342-348
-
-
Zhang, Y.1
-
11
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000; 29: 291-325.
-
(2000)
Annu Rev Biophys Biomol Struct
, vol.29
, pp. 291-325
-
-
Martí-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sánchez, R.4
Melo, F.5
Sali, A.6
-
12
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
-
(1997)
J Mol Biol
, vol.268
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
13
-
-
30344488120
-
TASSER: An automated method for the prediction of protein tertiary structures in CASP6
-
Zhang Y, Arakaki AK, Skolnick J. TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005; 61(S7): 91-98.
-
(2005)
Proteins
, vol.61
, Issue.S7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
14
-
-
0034733381
-
Ab initio construction of protein tertiary structures using a hierarchical approach
-
Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol 2000; 300: 171-185.
-
(2000)
J Mol Biol
, vol.300
, pp. 171-185
-
-
Xia, Y.1
Huang, E.S.2
Levitt, M.3
Samudrala, R.4
-
15
-
-
60849124513
-
Generalized ensemble methods for de novo structure prediction
-
Shmygelska A, Levitt M. Generalized ensemble methods for de novo structure prediction. Proc Natl Acad Sci USA 2009; 106: 1415-1420.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 1415-1420
-
-
Shmygelska, A.1
Levitt, M.2
-
16
-
-
42449122271
-
Ranking predicted protein structures with support vector regression
-
Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins 2008; 71: 1175-1182.
-
(2008)
Proteins
, vol.71
, pp. 1175-1182
-
-
Qiu, J.1
Sheffler, W.2
Baker, D.3
Noble, W.S.4
-
17
-
-
0034031680
-
Effective energy functions for protein structure prediction
-
Lazaridis T, Karplus M. Effective energy functions for protein structure prediction. Curr Opin Struct Biol 2000; 10: 139-145.
-
(2000)
Curr Opin Struct Biol
, vol.10
, pp. 139-145
-
-
Lazaridis, T.1
Karplus, M.2
-
18
-
-
1842861587
-
Development of novel statistical potentials for protein fold recognition
-
Buchete NV, Straub JE, Thirumalai D. Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol 2004; 14: 225-232.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 225-232
-
-
Buchete, N.V.1
Straub, J.E.2
Thirumalai, D.3
-
19
-
-
33646011728
-
In quest of an empirical potential for protein structure prediction
-
Skolnick J. In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 2006; 16: 166-171.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 166-171
-
-
Skolnick, J.1
-
20
-
-
84986512474
-
CHARMM: a program for macromolecular energy minimization and dynamic calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamic calculations. J Comput Chem 1983; 4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
21
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1998; 288: 477-487.
-
(1998)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
22
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990; 112: 6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
23
-
-
2942532422
-
Development and testing of a general Amber force field
-
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general Amber force field. J Comput Chem 2004; 25: 1157-1174.
-
(2004)
J Comput Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
24
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham TE, 3rd, Darden T, Gohlke H, Luo R, Merz KMJr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. J Comput Chem 2005; 26: 1668-1688.
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham 3rd, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
25
-
-
0037133165
-
A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field
-
Liwo A, ArlDukowicz P, Czaplewski C, OlDdziej S, Pillardy J, Scheraga HA. A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci USA 2002; 99: 1937-1942.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1937-1942
-
-
Liwo, A.1
ArlDukowicz, P.2
Czaplewski, C.3
OlDdziej, S.4
Pillardy, J.5
Scheraga, H.A.6
-
26
-
-
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. Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J Comput Chem 2007; 28: 2059-2066.
-
(2007)
J Comput Chem
, vol.28
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
27
-
-
46149096463
-
Protein model refinement using an optimized physics-based all-atom force field
-
Jagielska A, Wroblewska L, Skolnick J. Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci USA 2008; 105: 8268-8273.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 8268-8273
-
-
Jagielska, A.1
Wroblewska, L.2
Skolnick, J.3
-
28
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976; 9: 945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
29
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
-
Miyazawa S, Jernigan RL. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985; 18: 534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
30
-
-
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. 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 1990; 213: 859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
31
-
-
34247140654
-
Knowledge-based energy functions for computational studies of proteins
-
In: Xu Y,Xu D,Liang J, editors. New York: Springer
-
Li X, Liang J. Knowledge-based energy functions for computational studies of proteins. In: Xu Y, Xu D, Liang J, editors. Computational methods for protein structure prediction and modeling, Vol. 1. New York: Springer; 2006. pp 71-124.
-
(2006)
Computational methods for protein structure prediction and modeling, Vol. 1
, pp. 71-124
-
-
Li, X.1
Liang, J.2
-
32
-
-
51349134973
-
Refining homology models by combining replica-exchange molecular dynamics and statistical potentials
-
Zhu J, Fan H, Periole X, Honig B, Mark AE. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 2008; 72: 1171-1188.
-
(2008)
Proteins
, vol.72
, pp. 1171-1188
-
-
Zhu, J.1
Fan, H.2
Periole, X.3
Honig, B.4
Mark, A.E.5
-
33
-
-
0026785519
-
Contact potential that recognizes the correct folding of globular proteins
-
Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992; 227: 876-888.
-
(1992)
J Mol Biol
, vol.227
, pp. 876-888
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
34
-
-
0034308163
-
Distance-dependent, pair potential for protein folding: results from linear optimization
-
Tobi D, Elber R. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins 2000; 41: 40-46.
-
(2000)
Proteins
, vol.41
, pp. 40-46
-
-
Tobi, D.1
Elber, R.2
-
35
-
-
24344479166
-
Atomically detailed potentials to recognize native and approximate protein structures
-
Qiu J, Elber R. Atomically detailed potentials to recognize native and approximate protein structures. Proteins 2005; 61: 44-55.
-
(2005)
Proteins
, vol.61
, pp. 44-55
-
-
Qiu, J.1
Elber, R.2
-
36
-
-
38549146473
-
Distance dependent centroid to centroid force fields using high resolution decoys
-
Rajgaria R, McAllister SR, Floudas CA. Distance dependent centroid to centroid force fields using high resolution decoys. Proteins 2008; 70: 950-970.
-
(2008)
Proteins
, vol.70
, pp. 950-970
-
-
Rajgaria, R.1
McAllister, S.R.2
Floudas, C.A.3
-
37
-
-
0029945395
-
How optimization of potential function affects protein folding
-
Hao MH, Scheraga HA. How optimization of potential function affects protein folding. Proc Natl Acad Sci USA 1996; 93: 4984-4989
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 4984-4989
-
-
Hao, M.H.1
Scheraga, H.A.2
-
38
-
-
0034635955
-
A statistical mechanical method to optimize energy functions for protein folding
-
Bastolla U, Vendruscolo M, Knapp EW. A statistical mechanical method to optimize energy functions for protein folding. Proc Natl Acad Sci USA 2000; 97: 3977-3981.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 3977-3981
-
-
Bastolla, U.1
Vendruscolo, M.2
Knapp, E.W.3
-
39
-
-
0030596063
-
How to derive a protein folding potential? A new approach to an old problem
-
Mimy LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 1996; 264: 1164-1179.
-
(1996)
J Mol Biol
, vol.264
, pp. 1164-1179
-
-
Mimy, L.A.1
Shakhnovich, E.I.2
-
40
-
-
0031892528
-
Protein fold recognition without Boltzmann statistics or explicit physical basis
-
Huber T, Torda AE. Protein fold recognition without Boltzmann statistics or explicit physical basis. Protein Sci 1998; 7: 142-149.
-
(1998)
Protein Sci
, vol.7
, pp. 142-149
-
-
Huber, T.1
Torda, A.E.2
-
41
-
-
0032539910
-
Self-consistently optimized energy functions for protein structure prediction by molecular dynamics
-
Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proc Natl Acad Sci USA 1998; 95: 2932-2937.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2932-2937
-
-
Koretke, K.K.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
42
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas PD, Dill KA. Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 1996; 257: 457-469.
-
(1996)
J Mol Biol
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
44
-
-
0029909384
-
An iterative method for extracting energy-like quantities from protein structures
-
Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci USA 1996; 93: 11628-11633.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 11628-11633
-
-
Thomas, P.D.1
Dill, K.A.2
-
46
-
-
33746592898
-
Knowledgebased potentials in protein design
-
Poole AM, Ranganathan R. Knowledgebased potentials in protein design. Curr Opin Struct Biol 2006; 16: 508-513.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 508-513
-
-
Poole, A.M.1
Ranganathan, R.2
-
47
-
-
33749234779
-
What is a desirable statistical energy function for proteins and how can it be obtained?
-
Zhou Y, Zhou H, Zhang C, Liu S. What is a desirable statistical energy function for proteins and how can it be obtained? Cell Biochem Biophys 2006; 46: 165-174.
-
(2006)
Cell Biochem Biophys
, vol.46
, pp. 165-174
-
-
Zhou, Y.1
Zhou, H.2
Zhang, C.3
Liu, S.4
-
48
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
Shen M-Y, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006; 15: 2507-2524
-
(2006)
Protein Sci
, vol.15
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
-
49
-
-
38049051121
-
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing
-
Lu M, Dousis AD, Ma J. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol 2008; 376: 288-301.
-
(2008)
J Mol Biol
, vol.376
, pp. 288-301
-
-
Lu, M.1
Dousis, A.D.2
Ma, J.3
-
50
-
-
40549141792
-
QMEAN: a comprehensive scoring function for model quality assessment
-
Benkert P, Tosatto SCE, Schomburg D. QMEAN: a comprehensive scoring function for model quality assessment. Proteins 2008; 71: 261-277.
-
(2008)
Proteins
, vol.71
, pp. 261-277
-
-
Benkert, P.1
Tosatto, S.C.E.2
Schomburg, D.3
-
51
-
-
77955800755
-
Mean-force scoring functions for protein-ligand binding
-
Huang S-Y, Zou X. Mean-force scoring functions for protein-ligand binding. Annu Rep Comput Chem 2010; 6: 281-296.
-
(2010)
Annu Rep Comput Chem
, vol.6
, pp. 281-296
-
-
Huang, S.-Y.1
Zou, X.2
-
52
-
-
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. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
53
-
-
0035829446
-
Evaluation of docking functions for protein-ligand interactions
-
Perez C, Ortiz AR. Evaluation of docking functions for protein-ligand interactions. J Med Chem 2001; 44: 3768-3785.
-
(2001)
J Med Chem
, vol.44
, pp. 3768-3785
-
-
Perez, C.1
Ortiz, A.R.2
-
54
-
-
33750555073
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
-
Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 2006; 27: 1865-1875.
-
(2006)
J Comput Chem
, vol.27
, pp. 1865-1875
-
-
Huang, S.-Y.1
Zou, X.2
-
55
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
-
Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006; 27: 1876-1882.
-
(2006)
J Comput Chem
, vol.27
, pp. 1876-1882
-
-
Huang, S.-Y.1
Zou, X.2
-
56
-
-
7044247439
-
Determination of the interaction potential from the pair distribution function: an inverse Monte Carlo technique
-
(1-112026)
-
Almarza NG, Lomba E. Determination of the interaction potential from the pair distribution function: an inverse Monte Carlo technique. Phys Rev E 2003; 680: 11202(1-6).
-
(2003)
Phys Rev E
, vol.680
, pp. 11202
-
-
Almarza, N.G.1
Lomba, E.2
-
57
-
-
0002756891
-
A uniqueness theorem for fluid pair correlation functions
-
Henderson RL. A uniqueness theorem for fluid pair correlation functions. Phys Lett A 1974; 49: 197-198.
-
(1974)
Phys Lett A
, vol.49
, pp. 197-198
-
-
Henderson, R.L.1
-
58
-
-
36449000646
-
Transition states and folding dynamics of proteins and heteropolymers
-
Chan HS, Dill KA. Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 1994; 100: 9238-9257.
-
(1994)
J Chem Phys
, vol.100
, pp. 9238-9257
-
-
Chan, H.S.1
Dill, K.A.2
-
60
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: a synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 1995; 21: 167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
61
-
-
2442676589
-
Automated structure prediction of weakly homologous proteins on a genomic scale
-
Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004; 101: 7594-7599.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
62
-
-
0031576336
-
Torsion angle dynamics for NMR structure calculation with the new program DYANA
-
Güntert P, Mumenthaler C, Wüthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. JMol Biol 1997; 273: 283-298.
-
(1997)
JMol Biol
, vol.273
, pp. 283-298
-
-
Güntert, P.1
Mumenthaler, C.2
Wüthrich, K.3
-
63
-
-
33750050261
-
Development of a novel high resolution Ca-Ca distance dependent force field using a high quality decoy set
-
Rajgaria R, McAllister SR, Floudas CA. Development of a novel high resolution Ca-Ca distance dependent force field using a high quality decoy set. Proteins 2006; 65: 726-741.
-
(2006)
Proteins
, vol.65
, pp. 726-741
-
-
Rajgaria, R.1
McAllister, S.R.2
Floudas, C.A.3
-
64
-
-
46449084711
-
An iterative knowledge-based scoring function for protein-protein recognition
-
Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008; 72: 557-579.
-
(2008)
Proteins
, vol.72
, pp. 557-579
-
-
Huang, S.-Y.1
Zou, X.2
-
65
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai J, Bonneau R, Rohl C, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003; 53: 76-87.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.1
Bonneau, R.2
Rohl, C.3
Baker, D.4
-
66
-
-
0033853177
-
Decoys 'R' Us: a database of incorrect protein conformations to improve protein structure prediction
-
Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect protein conformations to improve protein structure prediction. Protein Sci 2000; 9: 1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
67
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
-
Park B, Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J Mol Biol 1996; 258: 367-392.
-
(1996)
J Mol Biol
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
68
-
-
0038708222
-
A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics
-
Keasar C, Levitt M. A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol 2003; 329: 159-174.
-
(2003)
J Mol Biol
, vol.329
, pp. 159-174
-
-
Keasar, C.1
Levitt, M.2
-
69
-
-
29244479220
-
A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
-
Fogolari F, Tosatto SCE, Colombo G. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinf 2005; 6: 301.
-
(2005)
BMC Bioinf
, vol.6
, pp. 301
-
-
Fogolari, F.1
Tosatto, S.C.E.2
Colombo, G.3
-
70
-
-
65549163966
-
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction
-
Handl J, Knowles J, Lovell SC. Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics 2009; 25: 1271-1279.
-
(2009)
Bioinformatics
, vol.25
, pp. 1271-1279
-
-
Handl, J.1
Knowles, J.2
Lovell, S.C.3
-
71
-
-
0346458791
-
A new pairwise folding potential based on improved decoy generation and side-chain packing
-
Loose C, Klepeis JL, Floudas CA. A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins 2004; 54: 303-314.
-
(2004)
Proteins
, vol.54
, pp. 303-314
-
-
Loose, C.1
Klepeis, J.L.2
Floudas, C.A.3
-
72
-
-
0028149160
-
Exploring conformational space with a simple lattice model for protein structure
-
Hinds DA, Levitt M. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 1994; 243: 668-682.
-
(1994)
J Mol Biol
, vol.243
, pp. 668-682
-
-
Hinds, D.A.1
Levitt, M.2
-
73
-
-
46449139781
-
Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions
-
Yang Y, Zhou Y. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions. Protein Sci 2008; 17: 1212-1219.
-
(2008)
Protein Sci
, vol.17
, pp. 1212-1219
-
-
Yang, Y.1
Zhou, Y.2
-
74
-
-
46449132707
-
Specific interactions for ab initio folding of protein terminal regions with secondary structures
-
Yang Y, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 2008; 72: 793-803.
-
(2008)
Proteins
, vol.72
, pp. 793-803
-
-
Yang, Y.1
Zhou, Y.2
-
75
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995; 117: 5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
76
-
-
14244273182
-
Theory and applications of the generalized Born solvation model in macromolecular simulations
-
Tsui V, Case DA. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 2001; 56: 275-291.
-
(2001)
Biopolymers
, vol.56
, pp. 275-291
-
-
Tsui, V.1
Case, D.A.2
-
77
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 1994; 98: 1978-1988.
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
78
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004; 57: 702-710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
79
-
-
0030054951
-
Delaunay tessellation of proteins: four body nearest neighbor propensities of amino acid residues
-
Tropsha A, Singh RK, Vaisman II. Delaunay tessellation of proteins: four body nearest neighbor propensities of amino acid residues. J Comput Biol 1996; 3: 213-222.
-
(1996)
J Comput Biol
, vol.3
, pp. 213-222
-
-
Tropsha, A.1
Singh, R.K.2
Vaisman, I.I.3
-
80
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations
-
Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from nonnative protein conformations. Bioinformatics 2003; 19: 1540-1548.
-
(2003)
Bioinformatics
, vol.19
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
81
-
-
19544391428
-
Geometric cooperativity and anticooperativity of three-body interactions in native proteins
-
Li X, Liang J. Geometric cooperativity and anticooperativity of three-body interactions in native proteins. Proteins 2005; 60: 46-65.
-
(2005)
Proteins
, vol.60
, pp. 46-65
-
-
Li, X.1
Liang, J.2
-
82
-
-
34249938371
-
Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
-
Feng YP, Kloczkowski A, Jernigan RL. Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys. Proteins 2007; 68: 57-66.
-
(2007)
Proteins
, vol.68
, pp. 57-66
-
-
Feng, Y.P.1
Kloczkowski, A.2
Jernigan, R.L.3
-
83
-
-
0030961726
-
Entropy in protein folding and in protein-protein interactions
-
Brady PG, Sharp KA. Entropy in protein folding and in protein-protein interactions. Curr Opin Struct Biol 1997; 7: 215-221.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 215-221
-
-
Brady, P.G.1
Sharp, K.A.2
-
84
-
-
77649221514
-
Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
-
Huang S-Y, Zou X. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. J Chem Inf Model 2010; 50: 262-273.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 262-273
-
-
Huang, S.-Y.1
Zou, X.2
|