메뉴 건너뛰기




Volumn 26, Issue 12, 2010, Pages 1493-1499

Ligand-binding site prediction of proteins based on known fragment-fragment interactions

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 77954185430     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq232     Document Type: Article
Times cited : (14)

References (32)
  • 1
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • Berman, H. et al. (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.
    • (2003) Nature Struct. Biol. , vol.10 , pp. 980
    • Berman, H.1
  • 2
    • 0035823226 scopus 로고    scopus 로고
    • SuperStar: Comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions
    • Boer, D.R. et al. (2001) SuperStar: Comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions. J. Mol. Biol., 312, 275-287.
    • (2001) J. Mol. Biol. , vol.312 , pp. 275-287
    • Boer, D.R.1
  • 3
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • Brady, G.P. and Stouten, P.F.W. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Comp. Aid. Mol. Des., 14, 383-401.
    • (2000) J. Comp. Aid. Mol. Des. , vol.14 , pp. 383-401
    • Brady, G.P.1    Stouten, P.F.W.2
  • 4
    • 0027219536 scopus 로고
    • Multiple copy simultaneous search and construction of ligands inbinding-sites-applicationtoinhibitorsofhiv-1asparticproteinase
    • Caflisch, A. et al. (1993) Multiple copy simultaneous search and construction of ligands inbinding-sites-applicationtoinhibitorsofhiv-1asparticproteinase. J.Med.Chem., 36, 2142-2167.
    • (1993) J. Med. Chem. , vol.36 , pp. 2142-2167
    • Caflisch, A.1
  • 5
    • 0038169950 scopus 로고    scopus 로고
    • Ligand binding: functional site location, similarity and docking
    • Campbell, S.J. et al. (2003) Ligand binding: functional site location, similarity and docking. Curr. Opin. Struct. Biol., 13, 389-395.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 389-395
    • Campbell, S.J.1
  • 6
    • 84988115618 scopus 로고
    • Validation of the general-purpose tripos 5.2 force-field
    • Clark, M. et al. (1989) Validation of the general-purpose tripos 5.2 force-field. J. Comput. Chem., 10, 982-1012.
    • (1989) J. Comput. Chem. , vol.10 , pp. 982-1012
    • Clark, M.1
  • 7
    • 0034651543 scopus 로고    scopus 로고
    • When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families
    • Denessiouk, K.A. and Johnson, M.S. (2000) When fold is not important: A common structural framework for adenine and AMP binding in 12 unrelated protein families. Protein Struct. Funct. Genet., 38, 310-326.
    • (2000) Protein Struct. Funct. Genet. , vol.38 , pp. 310-326
    • Denessiouk, K.A.1    Johnson, M.S.2
  • 8
    • 0035882572 scopus 로고    scopus 로고
    • Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins
    • Denessiouk, K. A. et al. (2001) Adenine recognition: A motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Protein Struct. Funct. Genet., 44, 282-291.
    • (2001) Protein Struct. Funct. Genet. , vol.44 , pp. 282-291
    • Denessiouk, K.A.1
  • 9
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke, H. et al. (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
  • 10
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation
    • Article no. 19
    • Huang, B.D. and Schroeder, M. (2006) LIGSITE(csc): predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol., 6, Article no. 19.
    • (2006) BMC Struct. Biol. , vol.6
    • Huang, B.D.1    Schroeder, M.2
  • 11
    • 85088686639 scopus 로고    scopus 로고
    • Sequence-based feature prediction and annotation of proteins
    • Juncker, A.S. et al. (2009) Sequence-based feature prediction and annotation of proteins. Genome Biol., 10,6.
    • (2009) Genome Biol , vol.10 , pp. 6
    • Juncker, A.S.1
  • 12
    • 33646228824 scopus 로고    scopus 로고
    • sc-PDB: an annotated database of druggable binding sites from the protein data bank
    • Kellenberger, E. et al. (2006) sc-PDB: an annotated database of druggable binding sites from the protein data bank. J. Chem. Inform. Model., 46, 717-727.
    • (2006) J. Chem. Inform. Model. , vol.46 , pp. 717-727
    • Kellenberger, E.1
  • 13
    • 0037832147 scopus 로고    scopus 로고
    • Protein informatics towards function identification
    • Kinoshita, K. and Nakamura, H. (2003) Protein informatics towards function identification. Curr. Opin. Struct. Biol., 13, 396-400.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 396-400
    • Kinoshita, K.1    Nakamura, H.2
  • 14
    • 14144254344 scopus 로고    scopus 로고
    • Identification of the ligand binding sites on the molecular surface of proteins
    • Kinoshita, K. and Nakamura, H. (2005) Identification of the ligand binding sites on the molecular surface of proteins. Protein Sci., 14, 711-718.
    • (2005) Protein Sci , vol.14 , pp. 711-718
    • Kinoshita, K.1    Nakamura, H.2
  • 15
    • 0032972775 scopus 로고    scopus 로고
    • Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes
    • Kinoshita, K. et al. (1999) Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes. Protein Engineer., 12, 11-14.
    • (1999) Protein Engineer , vol.12 , pp. 11-14
    • Kinoshita, K.1
  • 16
    • 0031032662 scopus 로고    scopus 로고
    • ATP binding proteins with different folds share a common ATP-binding structural motif
    • Kobayashi, N. and Go, N. (1997) ATP binding proteins with different folds share a common ATP-binding structural motif. Nat. Struct. Biol., 4, 6-7.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 6-7
    • Kobayashi, N.1    Go, N.2
  • 17
    • 3042545941 scopus 로고    scopus 로고
    • Identification, synthesis, and characterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site
    • Kristiansen, M. et al. (2004) Identification, synthesis, and characterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site. J. Med. Chem., 47, 3537-3545.
    • (2004) J. Med. Chem. , vol.47 , pp. 3537-3545
    • Kristiansen, M.1
  • 18
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    • Laurie, A.T.R. and Jackson, R.M. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916.
    • (2005) Bioinformatics , vol.21 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 19
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee, D. et al. (2007) Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol., 8, 995-1005.
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 995-1005
    • Lee, D.1
  • 20
    • 60749125063 scopus 로고    scopus 로고
    • Protein function annotation by homology-based inference
    • Loewenstein, Y. et al. (2009) Protein function annotation by homology-based inference. Genome Biol., 10, 207.
    • (2009) Genome Biol , vol.10 , pp. 207
    • Loewenstein, Y.1
  • 21
    • 52249097805 scopus 로고    scopus 로고
    • Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures
    • Morita, M. et al. (2008) Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Protein Struct. Funct. Bioinform., 73, 468-479.
    • (2008) Protein Struct. Funct. Bioinform. , vol.73 , pp. 468-479
    • Morita, M.1
  • 22
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility
    • Morris, G.M. et al. (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem., 30, 2785-2791.
    • (2009) J. Comput. Chem. , vol.30 , pp. 2785-2791
    • Morris, G.M.1
  • 23
    • 0033545622 scopus 로고    scopus 로고
    • Ageneral and fast scoring function for protein-ligand interactions: a simplified potential approach
    • Muegge, I. and Martin, Y.C. (1999) Ageneral 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
  • 24
    • 31544440473 scopus 로고    scopus 로고
    • An empirical approach for detecting nucleotide-binding sites on proteins
    • Saito, M. et al. (2006) An empirical approach for detecting nucleotide-binding sites on proteins. Protein Engineer. Des. Select., 19, 67-75.
    • (2006) Protein Engineer. Des. Select. , vol.19 , pp. 67-75
    • Saito, M.1
  • 25
    • 67651005449 scopus 로고    scopus 로고
    • The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
    • Schubert, C.R. and Stultz, C.M. (2009) The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design. J. Comput. Aid. Mol. Des., 23, 475-489.
    • (2009) J. Comput. Aid. Mol. Des. , vol.23 , pp. 475-489
    • Schubert, C.R.1    Stultz, C.M.2
  • 26
    • 0042880971 scopus 로고    scopus 로고
    • An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins
    • Shionyu-Mitsuyama, C. et al. (2003) An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins. Protein Engineer., 16, 467-478.
    • (2003) Protein Engineer , vol.16 , pp. 467-478
    • Shionyu-Mitsuyama, C.1
  • 27
    • 0036510961 scopus 로고    scopus 로고
    • Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design
    • Sotriffer, C. and Klebe, G. (2002) Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco, 57, 243-251.
    • (2002) Farmaco , vol.57 , pp. 243-251
    • Sotriffer, C.1    Klebe, G.2
  • 28
    • 0033757840 scopus 로고    scopus 로고
    • From structure to function: approaches and limitations
    • Thornton, J.M. et al. (2000) From structure to function: approaches and limitations. Nat. Struct. Biol., 7, 991-994.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 991-994
    • Thornton, J.M.1
  • 29
    • 9244232176 scopus 로고    scopus 로고
    • Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
    • Toyoshima, C. et al. (2004) Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues. Nature, 432, 361-368.
    • (2004) Nature , vol.432 , pp. 361-368
    • Toyoshima, C.1
  • 30
    • 0033047007 scopus 로고    scopus 로고
    • SuperStar: A knowledge-based approach for identifying interaction sites in proteins
    • Verdonk, M.L. et al. (1999) SuperStar: A knowledge-based approach for identifying interaction sites in proteins. J. Mol. Biol., 289, 1093-1108.
    • (1999) J. Mol. Biol. , vol.289 , pp. 1093-1108
    • Verdonk, M.L.1
  • 31
    • 0033395809 scopus 로고    scopus 로고
    • Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a
    • Vitali, J. et al. (1999) Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a. Acta Crystallogr. D. Biol. Crystallogr., 55, 1978-1985.
    • (1999) Acta Crystallogr. D. Biol. Crystallogr. , vol.55 , pp. 1978-1985
    • Vitali, J.1
  • 32
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou, H.Y. and Zhou, Y.Q. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.Y.1    Zhou, Y.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.