메뉴 건너뛰기




Volumn 2, Issue , 2012, Pages

A simple and efficient statistical potential for scoring ensembles of protein structures

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84859738455     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep00351     Document Type: Article
Times cited : (52)

References (54)
  • 1
    • 0017021957 scopus 로고
    • Mediumand long range interaction parameters between amino acids for predicting three dimensional structures of proteins
    • Tanaka, S. & Scheraga, H. A. Mediumand long range interaction parameters between amino acids for predicting three dimensional structures of proteins. Macromolecules 9, 945-950 (1976).
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 2
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures
    • Miyazawa, S., Miyazawa, S. & Jernigan, R. L. Estimation of effective interresidue contact energies from protein crystal structures. Macromolecules 18, 534-552 (1985).
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Miyazawa, S.2    Jernigan, R.L.3
  • 3
    • 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, M. J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular protiens. J. Mol. Biol. 213, 859-883 (1990). (Pubitemid 20213222)
    • (1990) Journal of Molecular Biology , vol.213 , Issue.4 , pp. 859-883
    • Sippl, M.J.1
  • 4
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure predictions
    • Lazaridis, T. & Karplus, M. Effective energy functions for protein structure predictions. Curr. Opin. Struct. Biol 10, 139-145 (1996).
    • (1996) Curr. Opin. Struct. Biol , vol.10 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 5
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • DOI 10.1006/jmbi.1997.0959
    • Simons, K. T., 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. 268, 209-225 (1997). (Pubitemid 27192690)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 6
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • DOI 10.1006/jmbi.1997.1479
    • Samudrala, R. & Moult, J. An all atom distance dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275, 895-916 (1998). (Pubitemid 28077703)
    • (1998) Journal of Molecular Biology , vol.275 , Issue.5 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 7
    • 38549146473 scopus 로고    scopus 로고
    • Distance dependent centroid to centroid force fields using high resolution decoys
    • DOI 10.1002/prot.21561
    • Rajgaria, R., McAllister, S. R. & Floudas, C. A. Distance dependent centroid to centroid force fields using high resolution decoys. Proteins 70, 950-970 (2008). (Pubitemid 351161953)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.3 , pp. 950-970
    • Rajgaria, R.1    McAllister, S.R.2    Floudas, C.A.3
  • 8
    • 42449129569 scopus 로고    scopus 로고
    • Information and discrimination in pairwise contact potentials
    • DOI 10.1002/prot.21733
    • Solis, A. D. & Rackovsky, S. Information and discrimination in pairwise contact potentials. Proteins 71, 1071-1087 (2008). (Pubitemid 351564035)
    • (2008) Proteins: Structure, Function and Genetics , vol.71 , Issue.3 , pp. 1071-1087
    • Solis, A.D.1    Rackovsky, S.2
  • 9
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. A new approach to protein fold recognition. Nature 358, 86-89 (1992).
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 10
    • 0032929780 scopus 로고    scopus 로고
    • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    • DOI 10.1002/(SICI)1097-0134(19990101)34:1 <82::AID-PROT7> 3.0.CO;2-A
    • Simons, K. T. et al. Improved Recognition of Native like Protein structures using a combination of sequence dependent and sequence independent features of proteins. Proteins 34, 82-95 (1999). (Pubitemid 29019533)
    • (1999) Proteins: Structure, Function and Genetics , vol.34 , Issue.1 , pp. 82-95
    • Simons, K.T.1    Ruczinski, I.2    Kooperberg, C.3    Fox, B.A.4    Bystroff, C.5    Baker, D.6
  • 11
    • 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. Protein 41, 40-56 (2000).
    • (2000) Protein , vol.41 , pp. 40-56
    • Tobi, D.1    Elber, R.2
  • 12
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • DOI 10.1002/prot.1087
    • Lu, H. & Skolnick, J. A distance dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44, 223-232 (2001). (Pubitemid 32702231)
    • (2001) Proteins: Structure, Function and Genetics , vol.44 , Issue.3 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 13
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • DOI 10.1002/prot.20007
    • Zhou, H. & Zhou, Y. Single body knowledge based potentials based energy score combined with sequence profile and secondary structure information for fold recognition, Protein 55, 1005-1013 (2004). (Pubitemid 38702957)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.4 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 14
    • 84859749126 scopus 로고    scopus 로고
    • Local propensities and statistical potentials of backbone and dhiedral angles in proteins
    • Betancourt, M. R. & Skolnick, J. Local propensities and statistical potentials of backbone and dhiedral angles in proteins. J. Mol. Biol. 235, 1598-1613 (2004).
    • (2004) J. Mol. Biol , vol.235 , pp. 1598-1613
    • Betancourt, M.R.1    Skolnick, J.2
  • 15
    • 33745152349 scopus 로고    scopus 로고
    • Protein refolding in silico with atom based statistical potentials and conformational search using a simple genetic algorithm
    • Fang, Q. & Shortle, D. Protein refolding in silico with atom based statistical potentials and conformational search using a simple genetic algorithm. J Mol. Biol. 395, 1456 (2006).
    • (2006) J Mol. Biol , vol.395 , pp. 1456
    • Fang, Q.1    Shortle, D.2
  • 16
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials of mean force for structure selection and stability
    • Skolnick, J., Jaroszewski, L., Kolinski, A. & Godzik, A. Derivation and testing of pair potentials of mean force for structure selection and stability. Protein Science 6, 676 (1997).
    • (1997) Protein Science , vol.6 , pp. 676
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 17
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • DOI 10.1110/ps.062416606
    • Shen, M. Y. & Sali, A. Statistical potentials for assessment and prediction of protein models and a survey of energy functions. Protein Science 15, 2507-2524 (2006). (Pubitemid 44771688)
    • (2006) Protein Science , vol.15 , Issue.11 , pp. 2507-2524
    • Shen, M.-Y.1    Sali, A.2
  • 18
    • 77949462824 scopus 로고    scopus 로고
    • New statistical potential for quality assessment of protein models and a survey of energy functions
    • Rykunov, D. & Fiser, A. New statistical potential for quality assessment of protein models and a survey of energy functions. BMC Bioinformatics 11, 128 (2010).
    • (2010) BMC Bioinformatics , vol.11 , pp. 128
    • Rykunov, D.1    Fiser, A.2
  • 19
    • 34147169516 scopus 로고    scopus 로고
    • Potential energy functions for protein design
    • DOI 10.1016/j.sbi.2007.03.006, PII S0959440X0700036X, Theory and Simulation / Mecromolecular Assemblages
    • Boas, F. E. & Harbury, P. B. Potential energy functions for protein design. Curr. Opin. Struct. Biol. 17, 199-204 (2007). (Pubitemid 46575252)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.2 , pp. 199-204
    • Boas, F.E.1    Harbury, P.B.2
  • 20
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    • DOI 10.1073/pnas.96.5.2025
    • Lee, J., Liwo, A. & Scheraga, H. A. Energy based de novo protein folding by conformational space annealing and off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal proteinAand to apo calbidin D9k. Proc. Natl. Acad. Sci. USA 96, 2025-2030 (1999). (Pubitemid 29117861)
    • (1999) Proceedings of the National Academy of Sciences of the United States of America , vol.96 , Issue.5 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 22
    • 67649101377 scopus 로고    scopus 로고
    • Generic coarse-grained model for protein folding and aggregation
    • Bereau, T. & Deserno, M. Generic coarse-grained model for protein folding and aggregation. J. Chem. Phys. 130, 235106 (2009).
    • (2009) J. Chem. Phys , vol.130 , pp. 235106
    • Bereau, T.1    Deserno, M.2
  • 23
    • 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 16, 166-171 (2006).
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 166-171
    • Skolnick, J.1
  • 24
    • 1842861587 scopus 로고    scopus 로고
    • Development of novel statistical potentials for protein folding recognition
    • Buchete, N. V., Straub, Thirumalai, D. Development of novel statistical potentials for protein folding recognition. Curr. Opin. Struct. Biol 14, 225-232 (2006).
    • (2006) Curr. Opin. Struct. Biol , vol.14 , pp. 225-232
    • Buchete, N.V.1    Straub Thirumalai, D.2
  • 25
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • DOI 10.1006/jmbi.1996.0256
    • Park, B. & Levitt, M. Energy functions that discriminate X-ray and near native folds from well constructed decoys. J. Mol. Biol 258, 367-392 (1996). (Pubitemid 26131738)
    • (1996) Journal of Molecular Biology , vol.258 , Issue.2 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 26
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
    • Samudrala, R. & Levitt, M. Decoy 'R' Us: a database of incorrect protein conformations to improve protein structure prediction. Protein Sci. 9, 1399-1401 (1998). (Pubitemid 30602295)
    • (2000) Protein Science , vol.9 , Issue.7 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 28
    • 74249102516 scopus 로고    scopus 로고
    • Evaluation of CASP8 model quality predictions
    • Cozzetto, D., Kryshtafovych, A. & Tramontano, A. Evaluation of CASP8 model quality predictions. Proteins 77, 157-166 (2009).
    • (2009) Proteins , vol.77 , pp. 157-166
    • Cozzetto, D.1    Kryshtafovych, A.2    Tramontano, A.3
  • 29
    • 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, S. C. Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction. Bioinformatics 25, 1271-1279 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1271-1279
    • Handl, J.1    Knowles, J.2    Lovell, S.C.3
  • 30
    • 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 Science 11, 2714 (2002).
    • (2002) Protein Science , vol.11 , pp. 2714
    • Zhou, H.1    Zhou, Y.2
  • 31
    • 0037452894 scopus 로고    scopus 로고
    • Discrimination of native protein structures using atomatom contact scoring
    • McConkey, B. J., Sobolev, Edelman, M. Discrimination of native protein structures using atomatom contact scoring. Proc. Natl. Acad. Sci. USA 100, 3215 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3215
    • McConkey, B.J.1    Sobolev Edelman, M.2
  • 32
    • 33747135021 scopus 로고    scopus 로고
    • Novel knowledge based mean force potential at the profile level
    • Dong, Q., Wang, X. & Lin, L. Novel knowledge based mean force potential at the profile level. BMC Bioinformatics 7: 324 (2006).
    • (2006) BMC Bioinformatics , vol.7 , pp. 324
    • Dong, Q.1    Wang, X.2    Lin, L.3
  • 33
    • 35348892593 scopus 로고    scopus 로고
    • A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    • DOI 10.1007/s12013-007-0050-5
    • Ferrada, E., Vergara, I. A. & Melo, F. Aknowledge based potential with an accurate description of local interactions improves discrimination between native and near native protein conformations. Cell Biochem Biophys. 49, 111-24 (2007). (Pubitemid 47574996)
    • (2007) Cell Biochemistry and Biophysics , vol.49 , Issue.2 , pp. 111-124
    • Ferrada, E.1    Vergara, I.A.2    Melo, F.3
  • 34
    • 38049051121 scopus 로고    scopus 로고
    • OPUS-PSP: An orientation dependent Statistical Allatom Potential derived from Side chain packing
    • Lou, M., Dousis, A. D. & Ma, J. OPUS-PSP: An orientation dependent Statistical Allatom Potential derived from Side chain packing. J. Mol. Biol. 376, 288-301 (2008).
    • (2008) J. Mol. Biol , vol.376 , pp. 288-301
    • Lou, M.1    Dousis, A.D.2    Ma, J.3
  • 35
    • 40549141792 scopus 로고    scopus 로고
    • QMEAN: A comprehensive scoring function for model quality assessment
    • Benkert, P., Tosatto, S. C. E. & Schomburg, D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins 71, 267-277 (2008).
    • (2008) Proteins , vol.71 , pp. 267-277
    • Benkert, P.1    Tosatto, S.C.E.2    Schomburg, D.3
  • 36
    • 67650358909 scopus 로고    scopus 로고
    • QMEAN server for protein quality estimation
    • Benkert, P., Kunzli, M. & Schwede, T. QMEAN server for protein quality estimation. Nucleic Acids Res. 37, 510-514 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. 510-514
    • Benkert, P.1    Kunzli, M.2    Schwede, T.3
  • 37
    • 37349067381 scopus 로고    scopus 로고
    • Dissecting contact potentials for proteins: Relative contributions of individual amino acids
    • DOI 10.1002/prot.21538
    • Buchete, N.-V., Straub, J. E. & Thirumalai, D. Dissecting contact potentials for proteins: Relative contributions of individual amino acids. Proteins 70, 119-130 (2008). (Pubitemid 350293454)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.1 , pp. 119-130
    • Buchete, N.-V.1    Straub, J.E.2    Thirumalai, D.3
  • 38
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713 (1983).
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 39
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • DOI 10.1093/nar/gkg571
    • Zemla, A. LGA: a method for finding 3d similarities in protein structures. Nucl. Ac. Res. 31, 3370-3374 (2003). (Pubitemid 37442162)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3370-3374
    • Zemla, A.1
  • 40
    • 0034799915 scopus 로고    scopus 로고
    • Cunning simplicity of protein folding landscapes
    • Bogatyreva, N. S. & Finkelstein AV. Cunning simplicity of protein folding landscapes. Prot, Eng. 14, 521-523 (2001). (Pubitemid 32959474)
    • (2001) Protein Engineering , vol.14 , Issue.8 , pp. 521-523
    • Bogatyreva, N.S.1    Finkelstein, A.V.2
  • 41
    • 0642340510 scopus 로고    scopus 로고
    • Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
    • Berrera, M., Molinari, H. & Fogolari, F. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4, 8 (2003).
    • (2003) BMC Bioinformatics , vol.4 , pp. 8
    • Berrera, M.1    Molinari, H.2    Fogolari, F.3
  • 42
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure pattern recognition of hydrogen bonded and geometrical features
    • Kabsch, W. & Sander, C. Dictionary of protein secondary structure pattern recognition of hydrogen bonded and geometrical features. Biopolymers, 22, 2257-2637 (1983).
    • (1983) Biopolymers , vol.22 , pp. 2257-2637
    • Kabsch, W.1    Sander, C.2
  • 43
    • 33845978790 scopus 로고    scopus 로고
    • Insight into the structure of amyloid fibrils from the analysis of globular proteins
    • Trovato, A., Chiti, F., Maritan, A. & Seno, F. Insight into the structure of amyloid fibrils from the analysis of globular proteins. Plos Comp. Biol. 2, 1602-1618 (2006).
    • (2006) Plos Comp. Biol , vol.2 , pp. 1602-1618
    • Trovato, A.1    Chiti, F.2    Maritan, A.3    Seno, F.4
  • 46
    • 0037441653 scopus 로고    scopus 로고
    • Structure validation by Calpha geometry: Phi, psi and Cbeta deviation
    • Lovell, S. C. et al. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50, 437-50 (2003).
    • (2003) Proteins , vol.50 , pp. 437-450
    • Lovell, S.C.1
  • 48
    • 34249071886 scopus 로고    scopus 로고
    • A bias-exchange approach to protein folding
    • DOI 10.1021/jp0678731
    • Piana, S. & Laio, A. A bias-exchange approach to protein folding. J. Phys. Chem. B. 111, 4553-4559 (2007). (Pubitemid 46787652)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.17 , pp. 4553-4559
    • Piana, S.1    Laio, A.2
  • 49
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • DOI 10.1007/S008940100045
    • Lindahl, E., Hess, B. & van der Spoel, D. GROMACS 3. 0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7, 306-317 (2001). (Pubitemid 36153547)
    • (2001) Journal of Molecular Modeling , vol.7 , Issue.8 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 50
    • 77953513118 scopus 로고    scopus 로고
    • Improved side-chain torsion potentials for the Amber ff99SB protein force field
    • Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins: Struct., Funct., Bioinf. 78, 1950-1958 (2010).
    • (2010) Proteins: Struct., Funct., Bioinf , vol.78 , pp. 1950-1958
    • Lindorff-Larsen, K.1
  • 52
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • Onufriev, A., Bashford, D. & Case, D. A. Exploring protein native states and largescale conformational changes with a modified generalized born model. Proteins: Struct., Funct., Bioinf. 55, 383-394 (2004). (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 53
    • 84859758189 scopus 로고    scopus 로고
    • Exploring the universe of protein strucutres beyond the protein data bank
    • Cossio, P. et al. Exploring the universe of protein strucutres beyond the protein data bank. Plos Compt. Biol 6, 11 (2010).
    • (2010) Plos Compt. Biol , vol.6 , pp. 11
    • Cossio, P.1
  • 54
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew, N., Elofsson, A., Rychlewski, L. & Fischer, D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16, 776-85 (2000).
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.