메뉴 건너뛰기




Volumn 80, Issue 3, 2012, Pages 818-824

H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough?

Author keywords

Docking refinement; Hierarchical protocol; Implicit solvent; Near native solutions

Indexed keywords

ARTICLE; ATOMIC PARTICLE; HYDROGEN BOND; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; SAMPLING;

EID: 84856794664     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23239     Document Type: Article
Times cited : (11)

References (24)
  • 1
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information
    • Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J Am Chem Soc 2003; 125: 1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 2
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003; 12: 1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 3
    • 35449008122 scopus 로고    scopus 로고
    • Integrating statistical pair potentials into protein complex prediction
    • Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins 2007; 69: 511-520.
    • (2007) Proteins , vol.69 , pp. 511-520
    • Mintseris, J.1    Pierce, B.2    Wiehe, K.3    Anderson, R.4    Chen, R.5    Weng, Z.6
  • 4
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: current status of docking methods
    • Mendez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003; 52: 51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 5
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez 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
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 6
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd Edition
    • Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 2007; 69: 704-18.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Méndez, R.2    Wodak, S.J.3
  • 7
    • 77950591112 scopus 로고    scopus 로고
    • Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility
    • Borrelli KW, Cossins B, Guallar V. Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility. J Comp Chem 2010; 31: 1224-1235.
    • (2010) J Comp Chem , vol.31 , pp. 1224-1235
    • Borrelli, K.W.1    Cossins, B.2    Guallar, V.3
  • 8
    • 34147107263 scopus 로고    scopus 로고
    • Protein energy landscape exploration. A novel Monte Carlo technique. Implications on camphor ligand binding
    • Borrelli KW, Vitalis A, Alcantara R, Guallar V. Protein energy landscape exploration. A novel Monte Carlo technique. Implications on camphor ligand binding. J Chem Theory Comput 2005; 6: 1304-1311.
    • (2005) J Chem Theory Comput , vol.6 , pp. 1304-1311
    • Borrelli, K.W.1    Vitalis, A.2    Alcantara, R.3    Guallar, V.4
  • 9
    • 34250882254 scopus 로고    scopus 로고
    • pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • Cheng TM, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins: Struct Funct Bioinform 2007; 68: 503-515.
    • (2007) Proteins: Struct Funct Bioinform , vol.68 , pp. 503-515
    • Cheng, T.M.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 11
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    • May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008; 70: 794-809.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 12
    • 48249138715 scopus 로고    scopus 로고
    • How to efficiently include receptor flexibility during computational docking
    • May A, Sieker F, Zacharias M. How to efficiently include receptor flexibility during computational docking. Curr Comput Aided Drug Des 2008; 4: 143-153.
    • (2008) Curr Comput Aided Drug Des , vol.4 , pp. 143-153
    • May, A.1    Sieker, F.2    Zacharias, M.3
  • 13
    • 42449161827 scopus 로고    scopus 로고
    • The interface of protein-protein complexes: analysis of contacts and prediction of interactions
    • Bahadur RP, Zacharias M. The interface of protein-protein complexes: analysis of contacts and prediction of interactions. Cellul Mol Life Sci 2008; 65: 1059-1072.
    • (2008) Cellul Mol Life Sci , vol.65 , pp. 1059-1072
    • Bahadur, R.P.1    Zacharias, M.2
  • 14
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 503-519.
    • (2007) J Mol Biol , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 15
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics, and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 1997; 272: 106-120.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 17
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2010; 78: 3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 18
    • 0036310711 scopus 로고    scopus 로고
    • On the role of crystal packing forces in determining protein sidechain conformations
    • Jacobson MP, Friesner RA, Xiang Z, Honig B. On the role of crystal packing forces in determining protein sidechain conformations. J Mol Biol 2002; 320: 597-608.
    • (2002) J Mol Biol , vol.320 , pp. 597-608
    • Jacobson, M.P.1    Friesner, R.A.2    Xiang, Z.3    Honig, B.4
  • 20
    • 33847034125 scopus 로고    scopus 로고
    • Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling
    • Li X, Jacobson MP, Zhu K, Zhao S, Friesner RA. Assignment of polar states for protein amino acid residues using an interaction cluster decomposition algorithm and its application to high resolution protein structure modeling. Proteins Struct Funct Bioinform 2007; 66: 824-837.
    • (2007) Proteins Struct Funct Bioinform , vol.66 , pp. 824-837
    • Li, X.1    Jacobson, M.P.2    Zhu, K.3    Zhao, S.4    Friesner, R.A.5
  • 21
    • 2942597884 scopus 로고    scopus 로고
    • First-shell solvation of ion pairs: correction of systematic errors in implicit solvent models
    • Yu Z, Jacobson MP, Josovitz J, Rapp CS, Friesner RA. First-shell solvation of ion pairs: correction of systematic errors in implicit solvent models. J Phys Chem B 2004; 108: 6643-6654.
    • (2004) J Phys Chem B , vol.108 , pp. 6643-6654
    • Yu, Z.1    Jacobson, M.P.2    Josovitz, J.3    Rapp, C.S.4    Friesner, R.A.5
  • 22
    • 0030955263 scopus 로고    scopus 로고
    • Understanding the recognition of protein structural classes by amino acid composition
    • Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins 1997; 29: 172-185.
    • (1997) Proteins , vol.29 , pp. 172-185
    • Bahar, I.1    Atilgan, A.R.2    Jernigan, R.L.3    Erman, B.4
  • 23
    • 45749139232 scopus 로고    scopus 로고
    • Protein ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking
    • May A, Zacharias M. Protein ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem 2008; 51: 3499-3506.
    • (2008) J Med Chem , vol.51 , pp. 3499-3506
    • May, A.1    Zacharias, M.2
  • 24
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand H. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001; 14: 1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.