메뉴 건너뛰기




Volumn 79, Issue 6, 2011, Pages 1923-1929

Erratum to Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. [Proteins 79, 6, (2011) 1923-1929] DOI: 10.1002/prot.23015;Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Author keywords

Coarse grained models; Multibody potentials; Optimization; Protein modeling; Proteins; Statistical potentials; Threading

Indexed keywords

AMINO ACID;

EID: 79955737158     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24578     Document Type: Erratum
Times cited : (37)

References (40)
  • 1
  • 2
    • 69449084152 scopus 로고    scopus 로고
    • Quality Assessment of Protein Structure Models
    • Kihara D, Chen, andYang YD. Quality Assessment of Protein Structure Models. Curr Protein Pept Sci 2009; 10: 216-228.
    • (2009) Curr Protein Pept Sci , vol.10 , pp. 216-228
    • Kihara, D.1    Chen2    Yang, Y.D.3
  • 3
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
    • Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997; 6: 676-688.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 4
    • 67449108422 scopus 로고    scopus 로고
    • FINDSITE: a combined evolution/structure-based approach to protein function prediction
    • Skolnick J, Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 2009; 10: 378-391.
    • (2009) Brief Bioinform , vol.10 , pp. 378-391
    • Skolnick, J.1    Brylinski, M.2
  • 5
    • 62849107262 scopus 로고    scopus 로고
    • Protein structure prediction and model quality assessment
    • Kryshtafovych A, Fidelis K. Protein structure prediction and model quality assessment. Drug Discov Today 2009; 14: 386-393.
    • (2009) Drug Discov Today , vol.14 , pp. 386-393
    • Kryshtafovych, A.1    Fidelis, K.2
  • 6
    • 77950833121 scopus 로고    scopus 로고
    • Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Virus 1. Purine Nucleoside Phosphorylase Ubiquitin Specific Protease 7, and Histone Demethylases
    • Bellows ML, Floudas CA. Computational Methods for De novo Protein Design and its Applications to the Human Immunodeficiency Virus 1. Purine Nucleoside Phosphorylase Ubiquitin Specific Protease 7, and Histone Demethylases. Curr Drug Targets 2010; 11: 264-278.
    • (2010) Curr Drug Targets , vol.11 , pp. 264-278
    • Bellows, M.L.1    Floudas, C.A.2
  • 7
    • 70350334391 scopus 로고    scopus 로고
    • Computer-aided design of functional protein interactions
    • Mandell DJ, Kortemme T. Computer-aided design of functional protein interactions. Nat Chem Biol 2009; 5: 797-807.
    • (2009) Nat Chem Biol , vol.5 , pp. 797-807
    • Mandell, D.J.1    Kortemme, T.2
  • 8
    • 70349775833 scopus 로고    scopus 로고
    • Backbone flexibility in computational protein design
    • Mandell DJ, Kortemme T. Backbone flexibility in computational protein design. Curr Opin Biotechnol 2009; 20: 420-428.
    • (2009) Curr Opin Biotechnol , vol.20 , pp. 420-428
    • Mandell, D.J.1    Kortemme, T.2
  • 9
    • 65249143885 scopus 로고    scopus 로고
    • Enzyme (re)design: lessons from natural evolution and computation
    • Gerlt JA, Babbitt PC. Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 2009; 13: 10-18.
    • (2009) Curr Opin Chem Biol , vol.13 , pp. 10-18
    • Gerlt, J.A.1    Babbitt, P.C.2
  • 10
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • Vajda S, Kozakov D. Convergence and combination of methods in protein-protein docking. Curr Opin Struct Biol 2009; 19: 164-170.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 11
    • 61449172290 scopus 로고    scopus 로고
    • Computational Methods for Calculation of Ligand-Binding Affinity
    • de Azevedo WF, Dias R. Computational Methods for Calculation of Ligand-Binding Affinity. Curr Drug Targets 2008; 9: 1031-1039.
    • (2008) Curr Drug Targets , vol.9 , pp. 1031-1039
    • de Azevedo, W.F.1    Dias, R.2
  • 12
    • 41949102408 scopus 로고    scopus 로고
    • Predicting 3D Structures of Protein-Protein Complexes
    • Vakser IA, Kundrotas P. Predicting 3D Structures of Protein-Protein Complexes. Curr Pharm Biotechnol 2008; 9: 57-66.
    • (2008) Curr Pharm Biotechnol , vol.9 , pp. 57-66
    • Vakser, I.A.1    Kundrotas, P.2
  • 13
    • 41949111630 scopus 로고    scopus 로고
    • Recent Progress and Future Directions in Protein-Protein Docking
    • Ritchie DW. Recent Progress and Future Directions in Protein-Protein Docking. Curr Protein Pept Sci 2008; 9: 1-15.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 14
    • 64649101249 scopus 로고    scopus 로고
    • Long-timescale molecular dynamics simulations of protein structure and function
    • Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function Curr Opin Struct Biol 2009; 19: 120-127.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 120-127
    • Klepeis, J.L.1    Lindorff-Larsen, K.2    Dror, R.O.3    Shaw, D.E.4
  • 15
    • 49249124018 scopus 로고    scopus 로고
    • Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions
    • Roccatano D. Computer Simulations Study of Biomolecules in Non-Aqueous or Cosolvent/Water Mixture Solutions. Curr Protein Pept Sci 2008; 9: 407-426.
    • (2008) Curr Protein Pept Sci , vol.9 , pp. 407-426
    • Roccatano, D.1
  • 18
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction J Mol Biol 1998; 275: 895-916.
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 19
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001; 44: 223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 20
    • 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
  • 21
    • 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 1986; 18: 534-552.
    • (1986) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 22
    • 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
    • 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.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 23
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mena force: an approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mena 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
  • 24
    • 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
  • 25
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt M, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999; 8: 361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.1    Thirumalai, D.2
  • 26
    • 0030806961 scopus 로고    scopus 로고
    • Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment
    • Munson P, Singh RK. Statistical significance of hierarchical multi-body potentials based on Delaunay tessellation and their application in sequence-structure alignment. Protein Sci 1997; 6: 1467-1481.
    • (1997) Protein Sci , vol.6 , pp. 1467-1481
    • Munson, P.1    Singh, R.K.2
  • 27
    • 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
  • 28
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
    • Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 2003; 19: 1540-1548.
    • (2003) Bioinformatics , vol.19 , pp. 1540-1548
    • Krishnamoorthy, B.1    Tropsha, A.2
  • 29
    • 34249938371 scopus 로고    scopus 로고
    • Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys
    • Feng Y, 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.1    Kloczkowski, A.2    Jernigan, R.L.3
  • 30
    • 77949470074 scopus 로고    scopus 로고
    • Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials
    • Feng Y, Kloczkowski A, Jernigan R. Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials. BMC Bioinformatics 2010; 11: 92-95.
    • (2010) BMC Bioinformatics , vol.11 , pp. 92-95
    • Feng, Y.1    Kloczkowski, A.2    Jernigan, R.3
  • 31
    • 0030832809 scopus 로고    scopus 로고
    • Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
    • Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins 1997; 29: 292-308.
    • (1997) Proteins , vol.29 , pp. 292-308
    • Bahar, I.1    Kaplan, M.2    Jernigan, R.L.3
  • 32
    • 0033853177 scopus 로고    scopus 로고
    • Decoys "R". Us: a database of incorrect conformations to improve protein structure prediction
    • Samudrala R, Levitt M. Decoys "R". Us: a database of incorrect 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
  • 33
    • 2442665257 scopus 로고    scopus 로고
    • Protein decoy sets for evaluating energy functions
    • Gilis D. Protein decoy sets for evaluating energy functions. J Biomol Struct Dyn 2004; 21: 725-736.
    • (2004) J Biomol Struct Dyn , vol.21 , pp. 725-736
    • Gilis, D.1
  • 36
    • 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
  • 37
    • 35648988945 scopus 로고    scopus 로고
    • Benchmarking consensus model quality assessment for protein fold recognition
    • McGuffin L. Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics 2007; 8: 345.
    • (2007) BMC Bioinformatics , vol.8 , pp. 345
    • McGuffin, L.1
  • 38
    • 7044220745 scopus 로고    scopus 로고
    • Nature of driving force for protein folding: a result from analyzing the statistical potential
    • Li H, Tang C, Wingreen NS. Nature of driving force for protein folding: a result from analyzing the statistical potential. Phys Rev Letts 1997; 4: 765-768.
    • (1997) Phys Rev Letts , vol.4 , pp. 765-768
    • Li, H.1    Tang, C.2    Wingreen, N.S.3
  • 39
    • 0032960853 scopus 로고    scopus 로고
    • Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues
    • Miyazawa S, Jernigan RL. Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues. Proteins 1999; 34: 49-68.
    • (1999) Proteins , vol.34 , pp. 49-68
    • Miyazawa, S.1    Jernigan, R.L.2
  • 40
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
    • Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997;6: 676-688.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.