메뉴 건너뛰기




Volumn 68, Issue 2, 2007, Pages 503-515

PyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

Author keywords

ASA based desolvation; Atomic solvation parameter; Binding energy; CAPRI; Protein protein association; Rigid body docking

Indexed keywords

ARTICLE; COMPUTER PROGRAM; ELECTRICITY; ENTHALPY; GEOMETRY; MONTE CARLO METHOD; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCORING SYSTEM; SOLVATION;

EID: 34250882254     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21419     Document Type: Article
Times cited : (274)

References (30)
  • 1
    • 0037435031 scopus 로고    scopus 로고
    • From words to literature in structural proteomics
    • Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature 2003;422:216-225.
    • (2003) Nature , vol.422 , pp. 216-225
    • Sali, A.1    Glaeser, R.2    Earnest, T.3    Baumeister, W.4
  • 3
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 4
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 5
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 6
    • 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
  • 7
    • 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
  • 8
    • 0028575449 scopus 로고
    • Hydrophobic docking: A proposed enhancement to molecular recognition techniques
    • Vakser LA, Aflalo C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 1994;20:320-329.
    • (1994) Proteins , vol.20 , pp. 320-329
    • Vakser, L.A.1    Aflalo, C.2
  • 10
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 11
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ. 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.3
  • 12
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 13
    • 0034212826 scopus 로고    scopus 로고
    • BiGGER: A new (soft) docking algorithm for predicting protein interactions
    • Palma PN, Krippahl L, Wampler JE, Moura JJ. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000;39:372-384.
    • (2000) Proteins , vol.39 , pp. 372-384
    • Palma, P.N.1    Krippahl, L.2    Wampler, J.E.3    Moura, J.J.4
  • 14
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 15
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 16
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
    • (2002) Protein Sci , vol.11 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 17
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical 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.3
  • 18
    • 17344380633 scopus 로고    scopus 로고
    • ICM-DISCO docking by global energy optimization with fully flexible side-chains
    • Fernandez-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 19
    • 1542390499 scopus 로고    scopus 로고
    • Identification of protein-protein interaction sites from docking energy landscapes
    • Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
    • (2004) J Mol Biol , vol.335 , pp. 843-865
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 20
    • 21644447570 scopus 로고    scopus 로고
    • Improving CAPRI predictions: Optimized desolvation for rigid-body docking
    • Fernandez-Recio J, Abagyan R, Totrov M. Improving CAPRI predictions: optimized desolvation for rigid-body docking. Proteins 2005;60:308-313.
    • (2005) Proteins , vol.60 , pp. 308-313
    • Fernandez-Recio, J.1    Abagyan, R.2    Totrov, M.3
  • 22
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RLJ. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.J.3
  • 24
    • 0001962564 scopus 로고    scopus 로고
    • The molecular modelling toolkit: A new approach to molecular simulations
    • Hinsen K. The molecular modelling toolkit: a new approach to molecular simulations. J Comput Chem 2000;21:79-85.
    • (2000) J Comput Chem , vol.21 , pp. 79-85
    • Hinsen, K.1
  • 27
  • 28
    • 4143057133 scopus 로고    scopus 로고
    • Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I
    • Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
    • (2004) J Biol Chem , vol.279 , pp. 36022-36028
    • Sansen, S.1    De Ranter, C.J.2    Gebruers, K.3    Brijs, K.4    Courtin, C.M.5    Delcour, J.A.6    Rabijns, A.7
  • 29
    • 33645095436 scopus 로고    scopus 로고
    • Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment
    • Chelliah V, Blundell TL, Fernandez-Recio J. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol 2006;357:1669-1682.
    • (2006) J Mol Biol , vol.357 , pp. 1669-1682
    • Chelliah, V.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 30


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.