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Volumn 69, Issue 4, 2007, Pages 852-858

Prediction and scoring of docking poses with pyDock

Author keywords

CAPRI; Desolvation energy; Electrostatics; Protein protein docking; PyDock

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; GUANOSINE TRIPHOSPHATE; PROTEIN UBC9;

EID: 36749053938     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21796     Document Type: Conference Paper
Times cited : (44)

References (23)
  • 1
    • 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
  • 2
    • 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
  • 3
    • 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
  • 4
    • 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
  • 5
    • 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
  • 6
    • 10844235653 scopus 로고    scopus 로고
    • Optimal docking area: A new method for predicting protein-protein interaction sites
    • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134-143.
    • (2005) Proteins , vol.58 , pp. 134-143
    • Fernandez-Recio, J.1    Totrov, M.2    Skorodumov, C.3    Abagyan, R.4
  • 7
    • 34250882254 scopus 로고    scopus 로고
    • pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • Man-Kuang Cheng T, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007;68:503-515.
    • (2007) Proteins , vol.68 , pp. 503-515
    • Man-Kuang Cheng, T.1    Blundell, T.L.2    Fernandez-Recio, J.3
  • 8
    • 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
  • 9
    • 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
  • 11
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. 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.L.2
  • 12
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507-2524.
    • (2006) Protein Sci , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 13
  • 14
    • 0030767485 scopus 로고    scopus 로고
    • VERIFY3D: Assessment of protein models with three-dimensional profiles
    • Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Method Enzymol 1997;277: 396-404.
    • (1997) Method Enzymol , vol.277 , pp. 396-404
    • Eisenberg, D.1    Luthy, R.2    Bowie, J.U.3
  • 15
    • 0033966170 scopus 로고    scopus 로고
    • Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction
    • Ray MC, Germon P, Vianney A, Portalier R, Lazzaroni JC. Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction. J Bacteriol 2000;182:821-824.
    • (2000) J Bacteriol , vol.182 , pp. 821-824
    • Ray, M.C.1    Germon, P.2    Vianney, A.3    Portalier, R.4    Lazzaroni, J.C.5
  • 16
    • 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
  • 17
    • 0037077265 scopus 로고    scopus 로고
    • Identification of a substrate recognition site on Ubc9
    • Lin D, Tatham MH, Yu B, Kim S, Hay RT, Chen Y. Identification of a substrate recognition site on Ubc9. J Biol Chem 2002;277:21740-21748.
    • (2002) J Biol Chem , vol.277 , pp. 21740-21748
    • Lin, D.1    Tatham, M.H.2    Yu, B.3    Kim, S.4    Hay, R.T.5    Chen, Y.6
  • 20
    • 34247473840 scopus 로고    scopus 로고
    • Molecular mimicry enables competitive recruitment by a natively disordered protein
    • Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
    • (2007) J Am Chem Soc , vol.129 , pp. 4800-4807
    • Bonsor, D.A.1    Grishkovskaya, I.2    Dodson, E.J.3    Kleanthous, C.4
  • 23
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.