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Volumn 79, Issue 9, 2011, Pages 2648-2661

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

Author keywords

Distance dependent all atom potentials; Knowledge based; Protein structure prediction; Scoring function

Indexed keywords

PROTEIN;

EID: 80051564821     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23086     Document Type: Article
Times cited : (61)

References (84)
  • 3
    • 0034060287 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 12
    • 0031585984 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 21
    • 0033531959 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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
  • 25
    • 0037133165 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 76
    • 14244273182 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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