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Volumn 26, Issue 5, 2012, Pages 595-601

Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors

Author keywords

Docking; Fragment like compounds; Scoring function; Trypsin inhibitors; Virtual screening

Indexed keywords

DOCKING; ENRICHMENT FACTORS; FRAGMENT-LIKE COMPOUND; PERFORMANCE; SCORING FUNCTIONS; SCREENING PROTOCOL; SOFTWARE FUNCTIONS; TRAINING SETS; TRYPSIN INHIBITOR; VIRTUAL SCREENING;

EID: 84863111119     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9526-x     Document Type: Conference Paper
Times cited : (16)

References (30)
  • 1
    • 85029621770 scopus 로고    scopus 로고
    • Fragment-based approaches in virtual screening
    • Sotriffer C (ed) Wiley-VCH Verlag, Weinheim
    • Huang D, Caflisch A (2011) Fragment-based approaches in virtual screening. In: Sotriffer C (ed) Virtual screening. Wiley-VCH Verlag, Weinheim, pp 467-489
    • (2011) Virtual Screening , pp. 467-489
    • Huang, D.1    Caflisch, A.2
  • 2
    • 67650997041 scopus 로고    scopus 로고
    • Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using glide
    • Kawatkar S, Wang H, Czerminski R, Joseph-McCarthy D (2009) Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using glide. J Comput Aided Mol Des 23:527-539
    • (2009) J Comput Aided Mol Des , vol.23 , pp. 527-539
    • Kawatkar, S.1    Wang, H.2    Czerminski, R.3    Joseph-McCarthy, D.4
  • 3
    • 77954036921 scopus 로고    scopus 로고
    • Virtual fragment docking by Glide: A validation study on 190 protein-fragment complexes
    • Sandor M, Kiss R, Keseru GM (2010) Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes. J Chem Inf Model 50:1165-1172
    • (2010) J Chem Inf Model , vol.50 , pp. 1165-1172
    • Sandor, M.1    Kiss, R.2    Keseru, G.M.3
  • 4
  • 6
    • 80051794377 scopus 로고    scopus 로고
    • Fragment-based drug discovery: What really works
    • Warr W (2011) Fragment-based drug discovery: what really works. J Comput Aided Mol Des 25:599-605
    • (2011) J Comput Aided Mol Des , vol.25 , pp. 599-605
    • Warr, W.1
  • 7
    • 78650633021 scopus 로고    scopus 로고
    • Computational medicinal chemistry in fragment-based drug discovery: What, how and when
    • Rabal O, Urbano-Cuadrado M, Oyarzabal J (2010) Computational medicinal chemistry in fragment-based drug discovery: what, how and when. Future Med Chem 3:95-134
    • (2010) Future Med Chem , vol.3 , pp. 95-134
    • Rabal, O.1    Urbano-Cuadrado, M.2    Oyarzabal, J.3
  • 8
    • 77956308900 scopus 로고    scopus 로고
    • Binding-site assessment by virtual fragment screening
    • Huang N, Jacobson MP (2010) Binding-site assessment by virtual fragment screening. PLoS ONE 5:e10109
    • (2010) PLoS ONE , vol.5
    • Huang, N.1    Jacobson, M.P.2
  • 9
    • 80051799481 scopus 로고    scopus 로고
    • Design of a fragment library that maximally represents available chemical space
    • Schulz M, Landström J, Bright K, Hubbard R (2011) Design of a fragment library that maximally represents available chemical space. J Comput Aided Mol Des 25:611-620
    • (2011) J Comput Aided Mol Des , vol.25 , pp. 611-620
    • Schulz, M.1    Landström, J.2    Bright, K.3    Hubbard, R.4
  • 10
    • 67650999672 scopus 로고    scopus 로고
    • Lessons for fragment library design: Analysis of output from multiple screening campaigns
    • Chen IJ, Hubbard R (2009) Lessons for fragment library design: analysis of output from multiple screening campaigns. J Comput Aided Mol Des 23:603-620
    • (2009) J Comput Aided Mol Des , vol.23 , pp. 603-620
    • Chen, I.J.1    Hubbard, R.2
  • 12
    • 65349195698 scopus 로고    scopus 로고
    • Molecular docking and ligand specificity in fragment-based inhibitor discovery
    • Chen Y, Shoichet BK (2009) Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol 5:358-364
    • (2009) Nat Chem Biol , vol.5 , pp. 358-364
    • Chen, Y.1    Shoichet, B.K.2
  • 14
    • 31344459599 scopus 로고    scopus 로고
    • In silico fragment-based discovery of DPP-IV S1 pocket binders
    • DOI 10.1016/j.bmcl.2005.11.038, PII S0960894X05014605
    • Rummey C, Nordhoff S, Thiemann M, Metz G (2006) In silico fragment-based discovery of DPP-IV S1 pocket binders. Bioorg Med Chem Lett 16:1405-1409 (Pubitemid 43143031)
    • (2006) Bioorganic and Medicinal Chemistry Letters , vol.16 , Issue.5 , pp. 1405-1409
    • Rummey, C.1    Nordhoff, S.2    Thiemann, M.3    Metz, G.4
  • 15
    • 68149170106 scopus 로고    scopus 로고
    • Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring
    • Friedman R, Caflisch A (2009) Discovery of plasmepsin inhibitors by fragment-based docking and consensus scoring. ChemMedChem 4:1317-1326
    • (2009) ChemMedChem , vol.4 , pp. 1317-1326
    • Friedman, R.1    Caflisch, A.2
  • 18
    • 0345059376 scopus 로고    scopus 로고
    • Announcing the worldwide Protein Data Bank
    • DOI 10.1038/nsb1203-980
    • Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide protein data bank. Nat Struct Mol Biol 10:980 (Pubitemid 37500485)
    • (2003) Nature Structural Biology , vol.10 , Issue.12 , pp. 980
    • Berman, H.1    Henrick, K.2    Nakamura, H.3
  • 19
    • 0035955550 scopus 로고    scopus 로고
    • Factorising ligand affinity: A Combined thermodynamic and crystallographic study of trypsin and thrombin inhibition
    • DOI 10.1006/jmbi.2001.5062
    • Dullweber F, Stubbs MT, Musil D, Stürzebecher J, Klebe G (2001) Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J Mol Biol 313:593-614 (Pubitemid 33052290)
    • (2001) Journal of Molecular Biology , vol.313 , Issue.3 , pp. 593-614
    • Dullweber, F.1    Stubbs, M.T.2    Musil, D.3    Sturzebecher, J.4    Klebe, G.5
  • 20
    • 0035151738 scopus 로고    scopus 로고
    • Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors
    • DOI 10.1016/S0969-2126(00)00551-7, PII S0969212600005517
    • Nar H, Bauer M, Schmid A, Stassen J-M, Wienen W, Priepke HWM, Kauffmann IK, Ries UJ, Hauel NH (2001) Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors. Structure 9:29-37 (Pubitemid 32064347)
    • (2001) Structure , vol.9 , Issue.1 , pp. 29-37
    • Nar, H.1    Bauer, M.2    Schmid, A.3    Stassen, J.-M.4    Wienen, W.5    Priepke, H.W.M.6    Kauffmann, I.K.7    Ries, U.J.8    Hauel, N.H.9
  • 21
  • 23
    • 77952546712 scopus 로고    scopus 로고
    • Structural binding evidence of the trypanocidal drugs Berenil̊ and Pentacarinate active principles to a serine protease model
    • Perilo CS, Pereira MT, Santoro MM, Nagem RAP (2010) Structural binding evidence of the trypanocidal drugs Berenil̊ and Pentacarinate active principles to a serine protease model. Int J Biol Macromol 46:502-511
    • (2010) Int J Biol Macromol , vol.46 , pp. 502-511
    • Perilo, C.S.1    Pereira, M.T.2    Santoro, M.M.3    Nagem, R.A.P.4
  • 24
    • 0346022974 scopus 로고    scopus 로고
    • Understanding protein-ligand interactions: The price of protein flexibility
    • DOI 10.1016/j.jmb.2003.11.041
    • Rauh D, Klebe G, Stubbs MT (2004) Understanding proteinligand interactions: the price of protein flexibility. J Mol Biol 335:1325-1341 (Pubitemid 38077249)
    • (2004) Journal of Molecular Biology , vol.335 , Issue.5 , pp. 1325-1341
    • Rauh, D.1    Klebe, G.2    Stubbs, M.T.3
  • 28
    • 0035910273 scopus 로고    scopus 로고
    • X-ray crystallographic analyses of complexes between bovine β-trypsin and Schiff base copper(II) or iron(III) chelates
    • DOI 10.1006/jmbi.2000.4303
    • Toyota E, Ng KKS, Sekizaki H, Itoh K, Tanizawa K, James MNG (2001) X-ray crystallographic analyses of complexes between bovine β-trypsin and schiff base copper(II) or iron(III) chelates. J Mol Biol 305:471-479 (Pubitemid 33034614)
    • (2001) Journal of Molecular Biology , vol.305 , Issue.3 , pp. 471-479
    • Toyota, E.1    Ng, K.K.S.2    Sekizaki, H.3    Itoh, K.4    Tanizawa, K.5    James, M.N.G.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.