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Volumn 385, Issue 2, 2009, Pages 381-392

RosettaLigand Docking with Full Ligand and Receptor Flexibility

Author keywords

backbone flexibility; protein flexibility; Rosetta; small molecule docking

Indexed keywords

LIGAND; RECEPTOR PROTEIN;

EID: 58149094776     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.11.010     Document Type: Article
Times cited : (360)

References (27)
  • 1
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of protein-ligand interactions. Docking and scoring: successes and gaps
    • Leach A.R., Shoichet B.K., and Peishoff C.E. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J. Med. Chem. 49 (2006) 5851-5855
    • (2006) J. Med. Chem. , vol.49 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 2
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: current status and future challenges
    • Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: current status and future challenges. Proteins 65 (2006) 15-26
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 3
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg F., Morris G.M., Sanner M.F., Olson A.J., and Goodsell D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46 (2002) 34-40
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 4
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: efficient molecular docking considering protein structure variations
    • Claussen H., Buning C., Rarey M., and Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308 (2001) 377-395
    • (2001) J. Mol. Biol. , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 5
    • 34447550727 scopus 로고    scopus 로고
    • FLIPDock: docking flexible ligands into flexible receptors
    • Zhao Y., and Sanner M.F. FLIPDock: docking flexible ligands into flexible receptors. Proteins 68 (2007) 726-737
    • (2007) Proteins , vol.68 , pp. 726-737
    • Zhao, Y.1    Sanner, M.F.2
  • 6
  • 8
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: a practical alternative
    • Totrov M., and Abagyan R. Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 18 (2008) 178-184
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 9
    • 33750056673 scopus 로고    scopus 로고
    • ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
    • Meiler J., and Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65 (2006) 538-584
    • (2006) Proteins , vol.65 , pp. 538-584
    • Meiler, J.1    Baker, D.2
  • 10
  • 13
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.2    Baker, D.3
  • 16
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 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
  • 19
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97 (2000) 10383-10388
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 21
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang C., Bradley P., and Baker D. Protein-protein docking with backbone flexibility. J. Mol. Biol. 373 (2007) 503-519
    • (2007) J. Mol. Biol. , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 22
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci. 14 (2005) 1328-1339
    • (2005) Protein Sci. , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 23
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with Rosetta
    • Das R., and Baker D. Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 77 (2008) 363-382
    • (2008) Annu. Rev. Biochem. , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 24
    • 0034031680 scopus 로고    scopus 로고
    • Effective energy functions for protein structure prediction
    • Lazaridis T., and Karplus M. Effective energy functions for protein structure prediction. Curr. Opin. Struct. Biol. 10 (2000) 139-145
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 139-145
    • Lazaridis, T.1    Karplus, M.2
  • 25
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T., Morozov A.V., and Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326 (2003) 1239-1259
    • (2003) J. Mol. Biol. , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 26
    • 2342593131 scopus 로고    scopus 로고
    • Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
    • Morozov A.V., Kortemme T., Tsemekhman K., and Baker D. Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proc. Natl Acad. Sci. USA 101 (2004) 6946-6951
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6946-6951
    • Morozov, A.V.1    Kortemme, T.2    Tsemekhman, K.3    Baker, D.4
  • 27
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack R.L., and Cohen F.E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 6 (1997) 1661-6981
    • (1997) Protein Sci. , vol.6 , pp. 1661-6981
    • Dunbrack, R.L.1    Cohen, F.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.