메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

A pairwise residue contact area-based mean force potential for discrimination of native protein structure

Author keywords

[No Author keywords available]

Indexed keywords

FOLD RECOGNITION; INTERACTION FUNCTIONS; NATIVE STRUCTURES; ORIENTATION DEPENDENT; POTENTIAL OF MEAN FORCE; PROTEIN STRUCTURE PREDICTION; PROTEIN STRUCTURES; PROTEIN THREADING;

EID: 76749140453     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-16     Document Type: Article
Times cited : (13)

References (46)
  • 1
    • 0030914617 scopus 로고    scopus 로고
    • Comparison of database potentials and molecular mechanics force fields
    • 10.1016/S0959-440X(97)80025-5, 9094335
    • Moult J. Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol 1997, 7:194-199. 10.1016/S0959-440X(97)80025-5, 9094335.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 194-199
    • Moult, J.1
  • 2
    • 0030968991 scopus 로고    scopus 로고
    • Empirical potentials and functions for protein folding and binding
    • 10.1016/S0959-440X(97)80029-2, 9094333
    • Vajda S, Sippl M, Novotny J. Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol 1997, 7:222-228. 10.1016/S0959-440X(97)80029-2, 9094333.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 222-228
    • Vajda, S.1    Sippl, M.2    Novotny, J.3
  • 3
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • 10.1006/jmbi.1996.0704, 9000638
    • Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 1996, 264:1164-1179. 10.1006/jmbi.1996.0704, 9000638.
    • (1996) J Mol Biol , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 4
    • 0033117762 scopus 로고    scopus 로고
    • Designing potential energy functions for protein folding
    • 10.1016/S0959-440X(99)80026-8, 10322206
    • Hao MH, Scheraga HA. Designing potential energy functions for protein folding. Curr Opin Struct Biol 1999, 9:184-188. 10.1016/S0959-440X(99)80026-8, 10322206.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 184-188
    • Hao, M.H.1    Scheraga, H.A.2
  • 5
    • 0033566614 scopus 로고    scopus 로고
    • An empirical energy potential with a reference state for protein fold and sequence recognition
    • 10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829
    • Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999, 36:357-369. 10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829.
    • (1999) Proteins , vol.36 , pp. 357-369
    • Miyazawa, S.1    Jernigan, R.L.2
  • 6
    • 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, 10:145.
    • (2000) Curr Opin Struct Biol , vol.10 , pp. 145
    • Lazaridis, T.1    Karplus, M.2
  • 7
    • 0036681394 scopus 로고    scopus 로고
    • 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
    • 10.1002/prot.10171, 12112706
    • Felts AK, Gallicchio E, Wallqvist A, Levy RM. 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 2002, 48:404-422. 10.1002/prot.10171, 12112706.
    • (2002) Proteins , vol.48 , pp. 404-422
    • Felts, A.K.1    Gallicchio, E.2    Wallqvist, A.3    Levy, R.M.4
  • 8
    • 0037079585 scopus 로고    scopus 로고
    • Identifying native-like protein structures using physics-based potentials
    • 10.1002/jcc.10018, 11913380
    • Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. J Comput Chem 2002, 23:147-160. 10.1002/jcc.10018, 11913380.
    • (2002) J Comput Chem , vol.23 , pp. 147-160
    • Dominy, B.N.1    Brooks, C.L.2
  • 9
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • 10.1006/jmbi.1999.2685, 10329155
    • Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999, 288:477-487. 10.1006/jmbi.1999.2685, 10329155.
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 10
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
    • 10.1006/jmbi.1999.2583, 10191147
    • Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287:797-815. 10.1006/jmbi.1999.2583, 10191147.
    • (1999) J Mol Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 12
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution. Proteins
    • 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N, 10223287
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins. Proteins 1999, 35:133-152. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N, 10223287.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 13
  • 14
    • 0029912748 scopus 로고    scopus 로고
    • 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. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996, 118:11225-111236.
    • (1996) J Am Chem Soc , vol.118 , pp. 11225-111236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 15
    • 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
    • 10.1016/S0022-2836(05)80269-4, 2359125
    • 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. 10.1016/S0022-2836(05)80269-4, 2359125.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 16
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • 10.1016/0959-440X(95)80081-6, 7648326
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995, 5:229-235. 10.1016/0959-440X(95)80081-6, 7648326.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 17
    • 0026761547 scopus 로고
    • Folding protein alpha-carbon chains into compact forms by Monte Carlo methods
    • 10.1002/prot.340140310, 1438179
    • Covell DG. Folding protein alpha-carbon chains into compact forms by Monte Carlo methods. Proteins 1992, 14:409-420. 10.1002/prot.340140310, 1438179.
    • (1992) Proteins , vol.14 , pp. 409-420
    • Covell, D.G.1
  • 18
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: statistical potential and genetic algorithms
    • 10.1002/pro.5560020508, 2142494, 8495198
    • Sun S. Reduced representation model of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993, 2:762-785. 10.1002/pro.5560020508, 2142494, 8495198.
    • (1993) Protein Sci , vol.2 , pp. 762-785
    • Sun, S.1
  • 19
    • 0028351287 scopus 로고
    • An improved pair potential to recognize native protein folds
    • 10.1002/prot.340180306, 8202466
    • Bauer A, Beyer A. An improved pair potential to recognize native protein folds. Proteins 1994, 18:254-261. 10.1002/prot.340180306, 8202466.
    • (1994) Proteins , vol.18 , pp. 254-261
    • Bauer, A.1    Beyer, A.2
  • 20
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials and protein simulations
    • 10.1016/S0959-440X(96)80075-3, 8728652
    • Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Curr Opin Struct Biol 1996, 6:195-209. 10.1016/S0959-440X(96)80075-3, 8728652.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 195-209
    • Jernigan, R.L.1    Bahar, I.2
  • 21
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with a non-local atomic interaction energy
    • 10.1006/jmbi.1998.1665, 9571028
    • Melo F, Feytmans E. Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 1998, 277:1141-1152. 10.1006/jmbi.1998.1665, 9571028.
    • (1998) J Mol Biol , vol.277 , pp. 1141-1152
    • Melo, F.1    Feytmans, E.2
  • 22
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • 10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U, 10944392
    • Tobi D, Elber R. Distance-dependent, pair potential for protein folding: Results from linear optimization. Proteins 2000, 41:40-46. 10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U, 10944392.
    • (2000) Proteins , vol.41 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 23
    • 0036145846 scopus 로고    scopus 로고
    • Statistical potentials for fold assessment
    • 10.1110/ps.25502, 2373452, 11790853
    • Melo F, Sanchez R, Sali A. Statistical potentials for fold assessment. Protein Sci 2002, 11:430-448. 10.1110/ps.25502, 2373452, 11790853.
    • (2002) Protein Sci , vol.11 , pp. 430-448
    • Melo, F.1    Sanchez, R.2    Sali, A.3
  • 24
    • 33747135021 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at the profile level
    • 10.1186/1471-2105-7-324, 1534065, 16803615
    • Dong Q, Wang X, Lin L. Novel knowledge-based mean force potential at the profile level. BMC Bioinformatics 2006, 7:324. 10.1186/1471-2105-7-324, 1534065, 16803615.
    • (2006) BMC Bioinformatics , vol.7 , pp. 324
    • Dong, Q.1    Wang, X.2    Lin, L.3
  • 25
    • 0042921442 scopus 로고    scopus 로고
    • How well can we predict native contacts in proteins based on decoy structures and their energies?
    • 10.1002/prot.10444, 12910459
    • Zhu J, Zhu Q, Shi Y, Liu H. How well can we predict native contacts in proteins based on decoy structures and their energies?. Proteins 2003, 52:598-608. 10.1002/prot.10444, 12910459.
    • (2003) Proteins , vol.52 , pp. 598-608
    • Zhu, J.1    Zhu, Q.2    Shi, Y.3    Liu, H.4
  • 26
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of native protein structures using atom-atom contact scoring
    • McConkey BJ, Sobolev V, Edelman M. Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A 2003, 100:3215-3220.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 3215-3220
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 27
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • 10.1110/ps.03348304, 2286718, 14739325
    • Zhang C, Liu S, Zhou H, Zhou Y. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci 2004, 13:400-411. 10.1110/ps.03348304, 2286718, 14739325.
    • (2004) Protein Sci , vol.13 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 28
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • 10.1073/pnas.0509355103, 1459360, 16567638
    • Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci 2006, 103:5361-5366. 10.1073/pnas.0509355103, 1459360, 16567638.
    • (2006) Proc Natl Acad Sci , vol.103 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 29
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • 10.1006/jmbi.1997.0959, 9149153
    • 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. 10.1006/jmbi.1997.0959, 9149153.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 30
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • 10.1110/ps.062416606, 2242414, 17075131
    • Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006, 15:2507-2524. 10.1110/ps.062416606, 2242414, 17075131.
    • (2006) Protein Sci , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 31
    • 34247356171 scopus 로고    scopus 로고
    • Scoring predictive models using a reduced representation of proteins: model and energy definition
    • 10.1186/1472-6807-7-15, 1854906, 17378941
    • Fogolari F, Pieri L, Dovier A, Bortolussi L, Giugliarelli G, Corazza A, Esposito G, Viglino P. Scoring predictive models using a reduced representation of proteins: model and energy definition. BMC Struct Biol 2007, 7:15. 10.1186/1472-6807-7-15, 1854906, 17378941.
    • (2007) BMC Struct Biol , vol.7 , pp. 15
    • Fogolari, F.1    Pieri, L.2    Dovier, A.3    Bortolussi, L.4    Giugliarelli, G.5    Corazza, A.6    Esposito, G.7    Viglino, P.8
  • 32
    • 70349448457 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys
    • 10.1002/prot.22457, 19452553
    • Mirzaie M, Eslahchi C, Pezeshk H, Sadeghi M. A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys. Proteins 2009, 77:454-463. 10.1002/prot.22457, 19452553.
    • (2009) Proteins , vol.77 , pp. 454-463
    • Mirzaie, M.1    Eslahchi, C.2    Pezeshk, H.3    Sadeghi, M.4
  • 33
    • 0344980731 scopus 로고    scopus 로고
    • Simplicial edge representation of protein structures and alpha contact potential with confidence measure
    • 10.1002/prot.10442, 14635122
    • Li X, Hu C, Liang J. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins 2003, 53:792-805. 10.1002/prot.10442, 14635122.
    • (2003) Proteins , vol.53 , pp. 792-805
    • Li, X.1    Hu, C.2    Liang, J.3
  • 34
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • 10.1006/jmbi.1996.0114, 8604144
    • Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996, 256:623-644. 10.1006/jmbi.1996.0114, 8604144.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 36
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • 2142698, 8019422
    • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994, 3:522-524. 2142698, 8019422.
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 38
    • 29244479220 scopus 로고    scopus 로고
    • A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
    • 10.1186/1471-2105-6-301, 1351271, 16354298
    • Fogolari F, Tosatto SC, Colombo G. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics 2005, 6:301. 10.1186/1471-2105-6-301, 1351271, 16354298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 301
    • Fogolari, F.1    Tosatto, S.C.2    Colombo, G.3
  • 39
    • 0026505184 scopus 로고
    • Evaluation of protein models by atomic solvation preference
    • 10.1016/0022-2836(92)91028-N, 1583696
    • Holm L, Sander C. Evaluation of protein models by atomic solvation preference. J Mol Biol 1992, 225:93-105. 10.1016/0022-2836(92)91028-N, 1583696.
    • (1992) J Mol Biol , vol.225 , pp. 93-105
    • Holm, L.1    Sander, C.2
  • 40
    • 3342936478 scopus 로고    scopus 로고
    • A comprehensive analysis of 40 blind protein structure predictions
    • 10.1186/1472-6807-2-3, 122083, 12150712
    • Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol 2002, 2:3-18. 10.1186/1472-6807-2-3, 122083, 12150712.
    • (2002) BMC Struct Biol , vol.2 , pp. 3-18
    • Samudrala, R.1    Levitt, M.2
  • 41
    • 0033853177 scopus 로고    scopus 로고
    • Decoys'R' Us:a database of incorrect conformation to improve protein structure prediction
    • 10.1110/ps.9.7.1399, 2144680, 10933507
    • Samudrala R, Levitt M. Decoys'R' Us:a database of incorrect conformation to improve protein structure prediction. Protein Sci 2000, 9:1399-1401. 10.1110/ps.9.7.1399, 2144680, 10933507.
    • (2000) Protein Sci , vol.9 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 42
    • 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, 285:367-392.
    • (1996) J Mol Biol , vol.285 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 43
    • 33750050261 scopus 로고    scopus 로고
    • A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set
    • 10.1002/prot.21149, 16981202
    • Rajgaria R, McAllister SR, Floudas CA. A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set. Proteins 2006, 65:726-741. 10.1002/prot.21149, 16981202.
    • (2006) Proteins , vol.65 , pp. 726-741
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 44
    • 0038008976 scopus 로고    scopus 로고
    • An improved protein decoy set for testing energy functions for protein structure prediction
    • 10.1002/prot.10454, 12945051
    • Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins 2003, 53:76-87. 10.1002/prot.10454, 12945051.
    • (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
  • 46
    • 47849103560 scopus 로고    scopus 로고
    • Decoy Discrimination Using Contact Potentials Based on Delaunay Tessellation of Hydrated Proteins
    • Reck GM, Vaisman II. Decoy Discrimination Using Contact Potentials Based on Delaunay Tessellation of Hydrated Proteins. IEEE Computer Society 2007, 159-167.
    • (2007) IEEE Computer Society , pp. 159-167
    • Reck, G.M.1    Vaisman, I.I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.