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Volumn 32, Issue 5, 2008, Pages 387-390

Protein ligand interaction database (PLID)

Author keywords

Binding pockets; Machine learning techniques; Motifs; Quantum chemical descriptors

Indexed keywords

CHEMICAL PROPERTIES; FLOW INTERACTIONS; LIGANDS; MECHANICAL PROPERTIES; PROTEINS;

EID: 49949100432     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2008.03.017     Document Type: Article
Times cited : (33)

References (28)
  • 1
    • 0037093507 scopus 로고    scopus 로고
    • Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling
    • Barolo S., and Posakony J.W. Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling. Genes Dev. 16 (2000) 1167-1181
    • (2000) Genes Dev. , vol.16 , pp. 1167-1181
    • Barolo, S.1    Posakony, J.W.2
  • 2
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman H.M., et al. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 3
    • 3142580346 scopus 로고    scopus 로고
    • PDBLIG: classification of small molecular protein binding in the protein data bank
    • Chalk A.J., et al. PDBLIG: classification of small molecular protein binding in the protein data bank. J. Med. Chem. 47 (2004) 3807-3816
    • (2004) J. Med. Chem. , vol.47 , pp. 3807-3816
    • Chalk, A.J.1
  • 4
    • 4043062916 scopus 로고    scopus 로고
    • De Novo drug design: integration of structure-based and ligand-based methods
    • Dean P.M., et al. De Novo drug design: integration of structure-based and ligand-based methods. Curr. Opin. Drug Discov. Dev. 7 (2004) 347-353
    • (2004) Curr. Opin. Drug Discov. Dev. , vol.7 , pp. 347-353
    • Dean, P.M.1
  • 5
    • 4544344217 scopus 로고    scopus 로고
    • Ligand depot: a data warehouse for ligands bound to macromolecules
    • Feng Z., et al. Ligand depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20 (2004) 2153-2155
    • (2004) Bioinformatics , vol.20 , pp. 2153-2155
    • Feng, Z.1
  • 6
    • 0037262054 scopus 로고    scopus 로고
    • Ligand-protein docking: cancer research at the interface between biology and chemistry
    • Glen R.C., and Allen S.C. Ligand-protein docking: cancer research at the interface between biology and chemistry. Curr. Med. Chem. 10 (2003) 763-767
    • (2003) Curr. Med. Chem. , vol.10 , pp. 763-767
    • Glen, R.C.1    Allen, S.C.2
  • 7
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke H., et al. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 295 (2000) 337-356
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1
  • 8
    • 33646254603 scopus 로고    scopus 로고
    • A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships
    • Gold N.D., and Jackson R.M. A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J. Chem. Inform. Model. 46 (2006) 736-742
    • (2006) J. Chem. Inform. Model. , vol.46 , pp. 736-742
    • Gold, N.D.1    Jackson, R.M.2
  • 9
    • 10844282814 scopus 로고    scopus 로고
    • MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites
    • Golovin A., et al. MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins 58 (2005) 190-199
    • (2005) Proteins , vol.58 , pp. 190-199
    • Golovin, A.1
  • 10
    • 23044480075 scopus 로고    scopus 로고
    • Binding MOAD (mother of all databases)
    • Hu L., et al. Binding MOAD (mother of all databases). Proteins 60 (2005) 333-340
    • (2005) Proteins , vol.60 , pp. 333-340
    • Hu, L.1
  • 11
    • 33646228824 scopus 로고    scopus 로고
    • sc-PDB: an annotated database of druggable binding sites from the protein data bank
    • Kellenberger E., et al. sc-PDB: an annotated database of druggable binding sites from the protein data bank. J. Chem. Inform. Model. 46 (2006) 717-727
    • (2006) J. Chem. Inform. Model. , vol.46 , pp. 717-727
    • Kellenberger, E.1
  • 12
    • 0028673158 scopus 로고
    • Protein-ligand interactions: exchange processes and determination of ligand conformation and protein-ligand contacts
    • Lian L.Y., et al. Protein-ligand interactions: exchange processes and determination of ligand conformation and protein-ligand contacts. Methods Enzymol. 239 (1994) 657-700
    • (1994) Methods Enzymol. , vol.239 , pp. 657-700
    • Lian, L.Y.1
  • 13
    • 33847317012 scopus 로고    scopus 로고
    • Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network
    • Malik A., and Ahmad S. Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network. BMC Struct. Biol. 7 (2007) 1-14
    • (2007) BMC Struct. Biol. , vol.7 , pp. 1-14
    • Malik, A.1    Ahmad, S.2
  • 14
    • 13444302754 scopus 로고    scopus 로고
    • EzCatDB: the enzyme-catalytic mechanism database
    • Nagano N. EzCatDB: the enzyme-catalytic mechanism database. Nucleic Acid. Res. 33 (2005) 407-412
    • (2005) Nucleic Acid. Res. , vol.33 , pp. 407-412
    • Nagano, N.1
  • 15
    • 13444272079 scopus 로고    scopus 로고
    • The CATH domain structure database and related resources gene3d and DHS provide comprehensive domain family information for genome analysis
    • Pearl F., et al. The CATH domain structure database and related resources gene3d and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 33 (2005) D247-D251
    • (2005) Nucleic Acids Res. , vol.33
    • Pearl, F.1
  • 16
    • 0031970446 scopus 로고    scopus 로고
    • Multi-ligand interactions with receptor-like protein tyrosine phosphates b: implications for intercellular signaling
    • Pelesa E., et al. Multi-ligand interactions with receptor-like protein tyrosine phosphates b: implications for intercellular signaling. Trends Biochem. Sci. 23 (1998) 121-124
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 121-124
    • Pelesa, E.1
  • 17
    • 0141506108 scopus 로고    scopus 로고
    • Protein ligand database (PLD): additional understanding of the nature and specificity of protein-ligand complexes
    • Puvanendrampillai D., and Mitchell J.B.O. Protein ligand database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 19 (2003) 1856-1857
    • (2003) Bioinformatics , vol.19 , pp. 1856-1857
    • Puvanendrampillai, D.1    Mitchell, J.B.O.2
  • 18
    • 33644783661 scopus 로고    scopus 로고
    • From subtle to substantial: role of metal ions on π-π interactions
    • Reddy A.S., et al. From subtle to substantial: role of metal ions on π-π interactions. J. Phys. Chem. B 110 (2006) 2479-2481
    • (2006) J. Phys. Chem. B , vol.110 , pp. 2479-2481
    • Reddy, A.S.1
  • 19
    • 34548288600 scopus 로고    scopus 로고
    • Virtual screening in drug discovery-a computational perspective
    • Reddy A.S., et al. Virtual screening in drug discovery-a computational perspective. Curr. Proteins Pept. Sci. 8 (2007) 329-351
    • (2007) Curr. Proteins Pept. Sci. , vol.8 , pp. 329-351
    • Reddy, A.S.1
  • 21
    • 0035950051 scopus 로고    scopus 로고
    • Ligand-protein database: linking protein-ligand complex structures to binding data
    • Roche O., et al. Ligand-protein database: linking protein-ligand complex structures to binding data. J. Med. Chem. 44 (2001) 3592-3598
    • (2001) J. Med. Chem. , vol.44 , pp. 3592-3598
    • Roche, O.1
  • 22
    • 0026054712 scopus 로고
    • Mechanisms of molecular recognition: investigations of organic host-guest complexes
    • Schneider H.-J. Mechanisms of molecular recognition: investigations of organic host-guest complexes. Angew. Chem. Int. Ed. 30 (1991) 1417-1436
    • (1991) Angew. Chem. Int. Ed. , vol.30 , pp. 1417-1436
    • Schneider, H.-J.1
  • 23
    • 13444256512 scopus 로고    scopus 로고
    • PDB-ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
    • Shin J.M., and Cho D.H. PDB-ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Res. 33 (2005) D238-D241
    • (2005) Nucleic Acids Res. , vol.33
    • Shin, J.M.1    Cho, D.H.2
  • 24
    • 33645886036 scopus 로고    scopus 로고
    • Exploring protein-ligand recognition with binding MOAD
    • Smith R.D., et al. Exploring protein-ligand recognition with binding MOAD. J. Mol. Graphics. Model. 24 (2006) 414-425
    • (2006) J. Mol. Graphics. Model. , vol.24 , pp. 414-425
    • Smith, R.D.1
  • 25
    • 34247265436 scopus 로고    scopus 로고
    • Use of amino acid composition to predict ligand-binding sites
    • Soga S., et al. Use of amino acid composition to predict ligand-binding sites. J. Chem. Inform. Model. 47 (2007) 400-406
    • (2007) J. Chem. Inform. Model. , vol.47 , pp. 400-406
    • Soga, S.1
  • 26
    • 0001306148 scopus 로고
    • Mechanisms of ligand recognition in myoglobin
    • Springer B.A., et al. Mechanisms of ligand recognition in myoglobin. Chem. Rev. 94 (1994) 699-714
    • (1994) Chem. Rev. , vol.94 , pp. 699-714
    • Springer, B.A.1
  • 27
    • 0036520840 scopus 로고    scopus 로고
    • A review of protein-small molecule docking methods
    • Taylor R.D., et al. A review of protein-small molecule docking methods. J. Comput. Aid. Mol. Des. 16 (2002) 151-166
    • (2002) J. Comput. Aid. Mol. Des. , vol.16 , pp. 151-166
    • Taylor, R.D.1
  • 28
    • 20444422149 scopus 로고    scopus 로고
    • The PDBbind database: methodologies and updates
    • Wang R., et al. The PDBbind database: methodologies and updates. J. Med. Chem. 48 (2005) 4111-4119
    • (2005) J. Med. Chem. , vol.48 , pp. 4111-4119
    • Wang, R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.