메뉴 건너뛰기




Volumn 4, Issue 8, 2009, Pages 1273-1278

Design, selection, and evaluation of a general kinase-focused library

Author keywords

General kinase model; Kinase focused library; Similarity; Virtual screening

Indexed keywords

PHOSPHOTRANSFERASE;

EID: 68149149021     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.200900164     Document Type: Article
Times cited : (16)

References (37)
  • 9
    • 43549112555 scopus 로고    scopus 로고
    • T. Fojo, Oncologist, 2008, 13, 277-283.
    • (2008) Oncologist , vol.13 , pp. 277-283
    • Fojo, T.1
  • 15
    • 68149158801 scopus 로고    scopus 로고
    • accessed May 21, 2009
    • Ensemble, Prous Science, 2002, http://www.prous.com (accessed May 21, 2009).
    • (2002) Ensemble
  • 18
    • 68149171378 scopus 로고    scopus 로고
    • accessed May 21, 2009
    • ChemAxon version 2.2, 2008, http://www.chemaxon.com (accessed May 21, 2009);
    • (2008) ChemAxon Version 2.2
  • 19
    • 68149156953 scopus 로고    scopus 로고
    • JChem Base was used for structure searching and chemical database access and management
    • JChem Base was used for structure searching and chemical database access and management: JChem v. 3.2.12, 2008;
    • (2008) JChem V. 3.2.12
  • 20
    • 68149165320 scopus 로고    scopus 로고
    • Marvin was used for drawing, displaying, and characterizing chemical structures and substructures: fingerprints are explained at: accessed May 21, 2009
    • Marvin was used for drawing, displaying, and characterizing chemical structures and substructures: Marvin v. 4.1.14, 2008; fingerprints are explained at: http://www.chemaxon.com/jchem/doc/user/fingerprint.html (accessed May 21, 2009).
    • (2008) Marvin V. 4.1.14
  • 24
    • 68149156952 scopus 로고    scopus 로고
    • Schrödinger, LLC, New York, NY (USA)
    • Glide version 40217, Schrödinger, LLC, New York, NY (USA).
    • Glide Version 40217
  • 25
    • 68149158803 scopus 로고    scopus 로고
    • The docking mode of Glide was used with the following parameters modified: maxconf=1000, maxkeep=5000, and maxref=1000
    • The docking mode of Glide was used with the following parameters modified: maxconf=1000, maxkeep=5000, and maxref=1000.
  • 34
    • 68149138346 scopus 로고    scopus 로고
    • note
    • The number of compounds docked is the number of compounds that pass the default docking filters (<100 atoms, <15 rotatable bonds, and no invalid atom types for the OPLS2001 force-field) and are thus smaller than the initial dataset size. For example, of the 150 reference compounds, eight were not docked due to the presence of too many rotatable bonds, giving a final set of 142 compounds which were evaluated by molecular docking.
  • 35
    • 68149168592 scopus 로고    scopus 로고
    • note
    • To identify ligand structures that are known protein kinase binders within the PDB, a set of five protein kinase crystal structures were identified as true protein kinase domains representing key sequences in the protein kinase family and used as reference sequences. The structures were 1ATP, 1NVR, 1OKY, 1QPD and 2BUJ. The co-crystal complexes with sequence identities of at least 20% over a span of at least 200 amino acids to the reference sequences were assumed to be true protein kinase structures, and their ligands true kinase binding molecules. Ligands co-crystallized with these kinase structures were extracted, and structures were eliminated if they contained undesirable elements, were trivial co-solvent molecules, ions or ATP-like compounds (consisting of an adenine or guanidine linked to a sugar moiety). This procedure ensured that our dataset consisted of ligands binding in the active site of protein or receptor kinases.
  • 37
    • 68149179216 scopus 로고    scopus 로고
    • note
    • A quinazoline modification of this scaffold was present in our reference set.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.