메뉴 건너뛰기




Volumn 19, Issue 14, 2003, Pages 1856-1857

L/D Protein Ligand Database (PLD): Additional understanding of the nature and specificity of protein-ligand complexes

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 0141506108     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg243     Document Type: Article
Times cited : (91)

References (17)
  • 1
    • 0033930882 scopus 로고    scopus 로고
    • BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways
    • Bader,G.D. and Hogue,C.W.V. (2000) BIND - a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics, 16, 465-477.
    • (2000) Bioinformatics , vol.16 , pp. 465-477
    • Bader, G.D.1    Hogue, C.W.V.2
  • 4
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Bohm,H.J. (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des., 8, 243-256.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 5
    • 0036169718 scopus 로고    scopus 로고
    • The Binding Database: Data management and interface design
    • Chen,X., Lin,Y., Liu,M. and Gilson,M.K. (2002) The Binding Database: data management and interface design. Bioinformatics, 18, 130-139.
    • (2002) Bioinformatics , vol.18 , pp. 130-139
    • Chen, X.1    Lin, Y.2    Liu, M.3    Gilson, M.K.4
  • 6
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke,H., Hendlich,M. and Klebe,G. (2000) Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol., 295, 337-356.
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 7
    • 0037142298 scopus 로고    scopus 로고
    • SMall Molecule Growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
    • Ishchenko,A.V. and Shakhnovich,E.I. (2002) SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem., 45, 2770-2780.
    • (2002) J. Med. Chem. , vol.45 , pp. 2770-2780
    • Ishchenko, A.V.1    Shakhnovich, E.I.2
  • 8
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones,G., Willett,P., Glen,R.C., Leach,A.R. and Taylor,R. (1997) Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 9
    • 0035498342 scopus 로고    scopus 로고
    • The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands
    • Mitchell,J.B.O. (2001) The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands. J. Chem. Inf. Comput. Sci., 41, 1617-1622.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1617-1622
    • Mitchell, J.B.O.1
  • 10
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential
    • Mitchell,J.B.O., Laskowski,R.A., Alex,A. and Thornton,J.M. (1999a) BLEEP - potential of mean force describing protein-ligand interactions: I. Generating potential. J. Comp. Chem., 20, 1165-1176.
    • (1999) J. Comp. Chem. , vol.20 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Thornton, J.M.4
  • 11
    • 0000882405 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
    • Mitchell,J.B.O., Laskowski,R.A., Alex,A., Forster,M.J. and Thornton,J.M. (1999b) BLEEP - potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data. J. Comp. Chem., 20, 1177-1185.
    • (1999) J. Comp. Chem. , vol.20 , pp. 1177-1185
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Forster, M.J.4    Thornton, J.M.5
  • 12
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris,G.M., Goodsell,D.S., Halliday,R.S., Huey,R., Hart,W.E., Belew,R.K. and Olson,A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comp. Chem., 19, 1639-1662.
    • (1998) J. Comp. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 13
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge,I. and Martin,Y.C. (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem., 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 14
    • 0035950051 scopus 로고    scopus 로고
    • Ligand-Protein DataBase: Linking protein-ligand complex structures to Binding Data
    • Roche,O., Kiyama,R. and Brooks,C.L. (2001) Ligand-Protein DataBase: linking protein-ligand complex structures to Binding Data. J. Med. Chem., 44, 3592-3598.
    • (2001) J. Med. Chem. , vol.44 , pp. 3592-3598
    • Roche, O.1    Kiyama, R.2    Brooks, C.L.3
  • 15
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 16
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions
    • Xenarios,I., Salwinski,L., Duan,X.J., Higney,P., Kim,S-M. and Eisenberg,D. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res., 30, 303-305.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 17
    • 0031552370 scopus 로고    scopus 로고
    • Determination of atomic desolvation energies from the structures of crystallized proteins
    • Zhang,C., Vasmatzis,G., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol., 267, 707-726.
    • (1997) J. Mol. Biol. , vol.267 , pp. 707-726
    • Zhang, C.1    Vasmatzis, G.2    Cornette, J.L.3    DeLisi, C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.