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Volumn 76, Issue 1, 2009, Pages 115-128

A generalized knowledge-based discriminatory function for biomolecular interactions

Author keywords

Biomolecular interactions; Complexes; Discriminatory function; Knowledge based; Protein dna; Protein ligand; Protein small molecule

Indexed keywords

ACCURACY; ARTICLE; COMPLEX FORMATION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION;

EID: 66249122733     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22323     Document Type: Article
Times cited : (21)

References (27)
  • 1
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • DOI 10.1038/nrd1549
    • Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 2004;3:935-949. (Pubitemid 39529931)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.11 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 2
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • DOI 10.1006/jmbi.1997.1479
    • Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916. (Pubitemid 28077703)
    • (1998) Journal of Molecular Biology , vol.275 , Issue.5 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 3
    • 26444588137 scopus 로고    scopus 로고
    • CSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
    • DOI 10.1021/jm050436v
    • Velec HF, Gohlke H, Klebe G. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 2005;48:6296-6303. (Pubitemid 41428984)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.20 , pp. 6296-6303
    • Velec, H.F.G.1    Gohlke, H.2    Klebe, G.3
  • 4
    • 33845976703 scopus 로고    scopus 로고
    • An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
    • DOI 10.1002/prot.21162
    • Robertson TA, Varani G. An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure. Proteins 2007;66:359-374. (Pubitemid 46053467)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.2 , pp. 359-374
    • Robertson, T.A.1    Varani, G.2
  • 5
    • 46449084711 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function for protein-protein recognition
    • Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
    • (2008) Proteins , vol.72 , pp. 557-579
    • Huang, S.-Y.1    Zou, X.2
  • 6
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883. (Pubitemid 20213222)
    • (1990) Journal of Molecular Biology , vol.213 , Issue.4 , pp. 859-883
    • Sippl, M.J.1
  • 7
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
    • Sippl MJ. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des 1993;7:473-501.
    • (1993) J Comput Aided Mol Des , vol.7 , pp. 473-501
    • Sippl, M.J.1
  • 9
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • DOI 10.1107/S0108768102003890
    • Allen FH. The Cambridge Structural Database: a quarter of amillion crystal structures and rising. Acta Crystallogr B 2002;58(3, Part 1):380-388. (Pubitemid 135702674)
    • (2002) Acta Crystallographica Section B: Structural Science , vol.58 , Issue.3 PART 1 , pp. 380-388
    • Allen, F.H.1
  • 13
    • 84986486653 scopus 로고
    • Determination of molecular topology and atomic hybridization states from heavy atom coordinates
    • Meng EC, Lewis RA. Determination of molecular topology and atomic hybridization states from heavy atom coordinates. J Comput Chem 1991;12:891-898.
    • (1991) J Comput Chem , vol.12 , pp. 891-898
    • Meng, E.C.1    Lewis, R.A.2
  • 15
    • 20544433165 scopus 로고
    • Van der Waals Volumes and Radii
    • Bondi A. van der Waals Volumes and Radii. J Phys Chem 1964;68:441-451.
    • (1964) J Phys Chem , vol.68 , pp. 441-451
    • Bondi, A.1
  • 16
    • 33748546968 scopus 로고    scopus 로고
    • Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals Radii
    • Rowland RS, Taylor R. Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii. J Phys Chem 1996;100:7384-7391. (Pubitemid 126789411)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.18 , pp. 7384-7391
    • Rowland, R.S.1    Taylor, R.2
  • 17
    • 84860150800 scopus 로고    scopus 로고
    • Available at [Accessed 1 February 2008]
    • Zhang J, Wang R. (Available at http://sw16.im.med.umich.edu/software/ xtool/) [Accessed 1 February 2008].
    • Zhang, J.1    Wang, R.2
  • 18
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • DOI 10.1021/jm0203783
    • Wang R, Lu Y, Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 2003;46:2287-2303. (Pubitemid 36637914)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.12 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 20
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • DOI 10.1021/jm049314d
    • Zhang C, Liu S, Zhu Q, Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem 2005;48:2325-2335. (Pubitemid 40516427)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 21
    • 33750574927 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
    • DOI 10.1002/jcc.20505
    • Huang S-Y, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 2006;27:1876-1882. (Pubitemid 44672569)
    • (2006) Journal of Computational Chemistry , vol.27 , Issue.15 , pp. 1876-1882
    • Huang, S.-Y.1    Zou, X.2
  • 22
    • 84860150801 scopus 로고    scopus 로고
    • Available at [Accessed 5 February 2008]
    • Robertson TA, Varani G. (Available at http://depts.washington.edu/ varani2/downloads/index.shtml) [Accessed 5 February 2008].
    • Robertson, T.A.1    Varani, G.2
  • 23
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • DOI 10.1006/jmbi.1997.1203
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120. (Pubitemid 27395541)
    • (1997) Journal of Molecular Biology , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 24
    • 52949098360 scopus 로고    scopus 로고
    • Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information
    • Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information. PLoS Comput Biol 2008;4:e1000181.
    • (2008) PLoS Comput Biol , vol.4
    • Wang, K.1    Horst, J.A.2    Cheng, G.3    Nickle, D.C.4    Samudrala, R.5
  • 25
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • DOI 10.1093/bioinformatics/bti315
    • Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908-1916. (Pubitemid 40668026)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.