메뉴 건너뛰기




Volumn 81, Issue 1, 2013, Pages 119-131

3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

Author keywords

Energy minimization; Hydrogen bonding network; Protein energy; Protein structure prediction; Protein structure refinement; Statistical potential

Indexed keywords

HYDROGEN;

EID: 84871034858     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24167     Document Type: Article
Times cited : (156)

References (54)
  • 1
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 2
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003; 51: 434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 3
    • 42149153292 scopus 로고    scopus 로고
    • A multi-template combination algorithm for protein comparative modeling
    • Cheng J. A multi-template combination algorithm for protein comparative modeling. BMC Struct Biol 2008; 8: 18.
    • (2008) BMC Struct Biol , vol.8 , pp. 18
    • Cheng, J.1
  • 4
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: a local meta-threading-server for protein structure prediction
    • Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res 2007; 35: 3375-3382.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 5
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007; 69: 108-117.
    • (2007) Proteins , vol.69 , pp. 108-117
    • Zhang, Y.1
  • 6
    • 36749030503 scopus 로고    scopus 로고
    • High accuracy template based modeling by global optimization
    • Joo K, Lee J, Lee S, Seo JH, Lee SJ. High accuracy template based modeling by global optimization. Proteins 2007; 69: 83-89.
    • (2007) Proteins , vol.69 , pp. 83-89
    • Joo, K.1    Lee, J.2    Lee, S.3    Seo, J.H.4    Lee, S.J.5
  • 7
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KMS, 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 USA 2006; 103: 5361-5366.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5361-5366
    • Misura, K.M.S.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 8
    • 56349095598 scopus 로고    scopus 로고
    • SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
    • Wang Q, Canutescu AA, Dunbrack RL. SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat Protoc 2008; 3: 1832-1847.
    • (2008) Nat Protoc , vol.3 , pp. 1832-1847
    • Wang, Q.1    Canutescu, A.A.2    Dunbrack, R.L.3
  • 9
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov GG, Shapovalov MV, Dunbrack RL, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009; 77: 778-795.
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack Jr, R.L.3
  • 10
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M. Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 1992; 226: 507-533.
    • (1992) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 12
    • 36049029967 scopus 로고    scopus 로고
    • High-resolution structure prediction and the crystallographic phase problem
    • Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. High-resolution structure prediction and the crystallographic phase problem. Nature 2007; 450: 259-264.
    • (2007) Nature , vol.450 , pp. 259-264
    • Qian, B.1    Raman, S.2    Das, R.3    Bradley, P.4    McCoy, A.J.5
  • 15
    • 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.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 8268
    • Jagielska, A.1    Wroblewska, L.2    Skolnick, J.3
  • 16
    • 33847673583 scopus 로고    scopus 로고
    • Near-native structure refinement using in vacuo energy minimization
    • Summa CM, Levitt M. Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 2007; 104: 3177.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 3177
    • Summa, C.M.1    Levitt, M.2
  • 17
    • 77955792980 scopus 로고    scopus 로고
    • Consistent refinement of submitted models at CASP using a knowledge-based potential
    • Chopra G, Kalisman N, Levitt M. Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins 2010; 78: 2668-2678.
    • (2010) Proteins , vol.78 , pp. 2668-2678
    • Chopra, G.1    Kalisman, N.2    Levitt, M.3
  • 18
    • 82955239912 scopus 로고    scopus 로고
    • Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
    • Zhang J, Liang Y, Zhang Y. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 2011; 19: 1784-1795.
    • (2011) Structure , vol.19 , pp. 1784-1795
    • Zhang, J.1    Liang, Y.2    Zhang, Y.3
  • 21
    • 0028929556 scopus 로고
    • Principles of protein folding--a perspective from simple exact models
    • Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, et al. Principles of protein folding--a perspective from simple exact models. Protein Sci 1995; 4: 561.
    • (1995) Protein Sci , vol.4 , pp. 561
    • Dill, K.A.1    Bromberg, S.2    Yue, K.3    Fiebig, K.M.4    Yee, D.P.5
  • 22
    • 47249116944 scopus 로고    scopus 로고
    • Understanding ensemble protein folding at atomic detail
    • Wallin S, Shakhnovich EI. Understanding ensemble protein folding at atomic detail. J Phys 2008; 20: 283101.
    • (2008) J Phys , vol.20 , pp. 283101
    • Wallin, S.1    Shakhnovich, E.I.2
  • 24
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J Mol Biol 1994; 238: 777-793.
    • (1994) J Mol Biol , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 25
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL, III. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007; 67: 922-930.
    • (2007) Proteins , vol.67 , pp. 922-930
    • Chen, J.1    Brooks III, C.L.2
  • 26
    • 0025398721 scopus 로고
    • WHAT IF: a molecular modeling and drug design program
    • Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990; 8: 52.
    • (1990) J Mol Graph , vol.8 , pp. 52
    • Vriend, G.1
  • 27
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison
    • Brünger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins 1988; 4: 148-156.
    • (1988) Proteins , vol.4 , pp. 148-156
    • Brünger, A.T.1    Karplus, M.2
  • 28
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation1
    • Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation1. J Mol Biol 1999; 285: 1735-1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 29
    • 69249137563 scopus 로고    scopus 로고
    • HAAD: a quick algorithm for accurate prediction of hydrogen atoms in protein structures
    • Li Y, Roy A, Zhang Y. HAAD: a quick algorithm for accurate prediction of hydrogen atoms in protein structures. PloS one 2009; 4: e6701.
    • (2009) PloS one , vol.4
    • Li, Y.1    Roy, A.2    Zhang, Y.3
  • 30
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun 1995; 91: 215-231.
    • (1995) Comput Phys Commun , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 31
    • 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 1983; 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 32
    • 44949104190 scopus 로고    scopus 로고
    • Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities
    • Amir EAD, Kalisman N, Keasar C. Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities. Proteins 2008; 72: 62-73.
    • (2008) Proteins , vol.72 , pp. 62-73
    • Amir, E.A.D.1    Kalisman, N.2    Keasar, C.3
  • 33
    • 33744802398 scopus 로고    scopus 로고
    • Effects of surface tethering on protein folding mechanisms
    • Friedel M, Baumketner A, Shea JE. Effects of surface tethering on protein folding mechanisms. Proc Natl Acad Sci USA 2006; 103: 8396-8401.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 8396-8401
    • Friedel, M.1    Baumketner, A.2    Shea, J.E.3
  • 34
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large scale optimization
    • Liu DC, Nocedal J. On the limited memory BFGS method for large scale optimization. Math Prog 1989; 45: 503-528.
    • (1989) Math Prog , vol.45 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 35
    • 0032606039 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP): round III
    • Moult J, Hubbard T, Fidelis K, Pedersen JT. Critical assessment of methods of protein structure prediction (CASP): round III. Proteins 1999; 37: 2-6.
    • (1999) Proteins , vol.37 , pp. 2-6
    • Moult, J.1    Hubbard, T.2    Fidelis, K.3    Pedersen, J.T.4
  • 36
    • 77951941264 scopus 로고    scopus 로고
    • MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8
    • Wang Z, Eickholt J, Cheng J. MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 2010; 26: 882-888.
    • (2010) Bioinformatics , vol.26 , pp. 882-888
    • Wang, Z.1    Eickholt, J.2    Cheng, J.3
  • 37
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003; 31: 3370-3374.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 38
    • 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
  • 39
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1976; 32: 922-923.
    • (1976) Acta Crystallogr A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 41
    • 36749099341 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions for template-based modeling targets
    • Kopp J, Bordoli L, Battey JND, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007; 69: 38-56.
    • (2007) Proteins , vol.69 , pp. 38-56
    • Kopp, J.1    Bordoli, L.2    Battey, J.N.D.3    Kiefer, F.4    Schwede, T.5
  • 42
    • 74249114654 scopus 로고    scopus 로고
    • Evaluation of template-based models in CASP8 with standard measures
    • Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, et al. Evaluation of template-based models in CASP8 with standard measures. Proteins 2009; 77: 18-28.
    • (2009) Proteins , vol.77 , pp. 18-28
    • Cozzetto, D.1    Kryshtafovych, A.2    Fidelis, K.3    Moult, J.4    Rost, B.5
  • 43
    • 74249092329 scopus 로고    scopus 로고
    • The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models
    • Keedy DA, Williams CJ, Headd JJ, Arendall IIIWB, Chen VB, et al. The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models. Proteins 2009; 77: 29-49.
    • (2009) Proteins , vol.77 , pp. 29-49
    • Keedy, D.A.1    Williams, C.J.2    Headd, J.J.3    Arendall III, W.B.4    Chen, V.B.5
  • 44
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci USA 1998; 95: 5913.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 5913
    • Levitt, M.1    Gerstein, M.2
  • 45
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TM-score= 0.5?
    • Xu J, Zhang Y. How significant is a protein structure similarity with TM-score= 0.5? Bioinformatics 2010; 26: 889-895.
    • (2010) Bioinformatics , vol.26 , pp. 889-895
    • Xu, J.1    Zhang, Y.2
  • 51
    • 0032410839 scopus 로고    scopus 로고
    • Packing of sidechains in low-resolution models for proteins
    • Keskin O, Bahar I. Packing of sidechains in low-resolution models for proteins. Fold Des 1998; 3: 469-479.
    • (1998) Fold Des , vol.3 , pp. 469-479
    • Keskin, O.1    Bahar, I.2
  • 52
  • 53
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Méndez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005; 60: 150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Méndez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 54
    • 2442677781 scopus 로고    scopus 로고
    • Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
    • Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics 2004; 20: 1087-1096.
    • (2004) Bioinformatics , vol.20 , pp. 1087-1096
    • Arakaki, A.K.1    Zhang, Y.2    Skolnick, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.