메뉴 건너뛰기




Volumn 7, Issue 4, 2010, Pages

Grid-derived structure-based 3D pharmacophores and their performance compared to docking

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER AIDED DESIGN; DRUG DESIGN; METABOLISM; MOLECULAR DOCKING; PHARMACOPHORE; SCREENING TEST; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; VIRTUAL SCREENING;

EID: 78650750776     PISSN: 17406749     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ddtec.2010.09.002     Document Type: Review
Times cited : (12)

References (33)
  • 1
    • 38149057519 scopus 로고    scopus 로고
    • Monty Kier and the origin of the pharmacophore concept
    • J.H. Van Drie Monty Kier and the origin of the pharmacophore concept Internet Electron. J. Mol. Des. 6 2007 271 279
    • (2007) Internet Electron. J. Mol. Des. , vol.6 , pp. 271-279
    • Van Drie, J.H.1
  • 2
    • 0000460468 scopus 로고
    • The conformational parameter in drug design: The active analog approach
    • G.R. Marshall The conformational parameter in drug design: the active analog approach E.C. Olson, R.E. Christoffersen, Computer-Assisted Drug Design 1979 American Chemical Society 205 226
    • (1979) Computer-Assisted Drug Design , pp. 205-226
    • Marshall, G.R.1
  • 3
    • 77249106566 scopus 로고    scopus 로고
    • Three-dimensional pharmacophore methods in drug discovery
    • A.R. Leach Three-dimensional pharmacophore methods in drug discovery J. Med. Chem. 53 2010 539 558
    • (2010) J. Med. Chem. , vol.53 , pp. 539-558
    • Leach, A.R.1
  • 4
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • P.J. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 28 1985 849 857
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 5
    • 78650757861 scopus 로고    scopus 로고
    • Molecular Discovery
    • Molecular Discovery: http://www.moldiscovery.com
  • 6
    • 73749087803 scopus 로고    scopus 로고
    • Molecular fields in drug discovery: Getting old or reaching maturity?
    • S. Cross Molecular fields in drug discovery: getting old or reaching maturity? Drug Discov. Today 15 2010 23 32
    • (2010) Drug Discov. Today , vol.15 , pp. 23-32
    • Cross, S.1
  • 7
    • 0020491251 scopus 로고
    • A geometric approach to macromolecule-ligand interactions
    • I.D. Kuntz A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 1982 269 288
    • (1982) J. Mol. Biol. , vol.161 , pp. 269-288
    • Kuntz, I.D.1
  • 8
    • 60549086155 scopus 로고    scopus 로고
    • Four-dimensional docking: A fast and accurate account of discrete receptor flexibility in ligand docking
    • G. Bottegoni Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking J. Med. Chem. 52 2009 397 406
    • (2009) J. Med. Chem. , vol.52 , pp. 397-406
    • Bottegoni, G.1
  • 10
    • 77951997162 scopus 로고    scopus 로고
    • Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap Method and free energy perturbation calculations
    • R.W Cristiano Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap Method and free energy perturbation calculations J. Chem. Inf. Model. 50 2010 547 559
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 547-559
    • Cristiano, R.W.1
  • 11
    • 40649094486 scopus 로고    scopus 로고
    • Towards improving compound selection in structure-based virtual screening
    • B. Waszkowycz Towards improving compound selection in structure-based virtual screening Drug Discov. Today 13 2008 219 226
    • (2008) Drug Discov. Today , vol.13 , pp. 219-226
    • Waszkowycz, B.1
  • 12
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery?
    • D.E. Clark What has virtual screening ever done for drug discovery? Expert Opin. Drug Discov. 3 2008 841 851
    • (2008) Expert Opin. Drug Discov. , vol.3 , pp. 841-851
    • Clark, D.E.1
  • 13
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • N. Huang Benchmarking sets for molecular docking J. Med. Chem. 49 2006 6789 6801
    • (2006) J. Med. Chem. , vol.49 , pp. 6789-6801
    • Huang, N.1
  • 15
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for evaluation of computational methods
    • A.N. Jain Recommendations for evaluation of computational methods J. Comput.-Aided Mol. Des. 22 2008 133 139
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 133-139
    • Jain, A.N.1
  • 16
    • 41349122416 scopus 로고    scopus 로고
    • Optimization of CAMD techniques 3. Virtual screening enrichment studies: A help or hindrance in tool selection?
    • A.C. Good Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? J. Comput.-Aided Mol. Des. 22 2008 169 178
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 169-178
    • Good, A.C.1
  • 17
    • 41349093326 scopus 로고    scopus 로고
    • What do we know and when do we know it?
    • A. Nicholls What do we know and when do we know it? J. Comput.-Aided Mol. Des. 22 2008 239 255
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 239-255
    • Nicholls, A.1
  • 18
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): Theory and application
    • M. Baroni A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): theory and application J. Chem. Inf. Model. 47 2007 279 294
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 279-294
    • Baroni, M.1
  • 19
    • 77956019866 scopus 로고    scopus 로고
    • FLAP: GRID molecular interaction fields in virtual screening: Validation using the DUD dataset
    • S. Cross FLAP: GRID molecular interaction fields in virtual screening: validation using the DUD dataset J. Chem. Inf. Model. 50 2010 1442 1450
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1442-1450
    • Cross, S.1
  • 20
    • 75749123456 scopus 로고    scopus 로고
    • High-throughput virtual screening of proteins using GRID molecular interaction fields
    • S. Sciabola High-throughput virtual screening of proteins using GRID molecular interaction fields J. Chem. Inf. Model. 50 2010 155 169
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 155-169
    • Sciabola, S.1
  • 21
    • 57549116404 scopus 로고    scopus 로고
    • Targets looking for drugs: A multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery
    • C. Tintori Targets looking for drugs: a multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery J. Chem. Inf. Model. 48 2008 2166 2179
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 2166-2179
    • Tintori, C.1
  • 22
    • 33845727607 scopus 로고    scopus 로고
    • Pocket v.2: Further developments on receptor-based pharmacophore modeling
    • J. Chen Pocket v.2: further developments on receptor-based pharmacophore modeling J. Chem. Inf. Model. 46 2006 2684 2691
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 2684-2691
    • Chen, J.1
  • 23
    • 33745584385 scopus 로고    scopus 로고
    • GBPM: GRID-based pharmacophore model: Concept and application studies to protein-protein recognition
    • F. Ortuso GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition Bioinformatics 22 2006 1449 1455
    • (2006) Bioinformatics , vol.22 , pp. 1449-1455
    • Ortuso, F.1
  • 24
    • 78650758557 scopus 로고    scopus 로고
    • Accelrys
    • Accelrys: http://www.accelrys.com/
  • 25
    • 77950654271 scopus 로고    scopus 로고
    • Computational analysis of human immunodeficiency virus (HIV) type-1 reverse transcriptase crystallographic models based on significant conserved residues found in highly active antiretroviral therapy (HAART)-treated patients
    • S. Alcaro Computational analysis of human immunodeficiency virus (HIV) type-1 reverse transcriptase crystallographic models based on significant conserved residues found in highly active antiretroviral therapy (HAART)-treated patients Curr. Med. Chem. 17 2010 290 308
    • (2010) Curr. Med. Chem. , vol.17 , pp. 290-308
    • Alcaro, S.1
  • 26
    • 67049169018 scopus 로고    scopus 로고
    • 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors
    • F. Falchi 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors Chem. Med. Chem. 4 2009 976 987
    • (2009) Chem. Med. Chem. , vol.4 , pp. 976-987
    • Falchi, F.1
  • 27
    • 78650752472 scopus 로고    scopus 로고
    • Cambridge Crystallographic Data Centre
    • Cambridge Crystallographic Data Centre: http://www.ccdc.cam.ac.uk/
  • 28
    • 33750970572 scopus 로고    scopus 로고
    • Receptor-based pharmacophores for serotonin 5-HT7R antagonists- implications to selectivity
    • M. Kołaczkowski Receptor-based pharmacophores for serotonin 5-HT7R antagonists-implications to selectivity J. Med. Chem. 49 2006 6732 6741
    • (2006) J. Med. Chem. , vol.49 , pp. 6732-6741
    • Kołaczkowski, M.1
  • 29
    • 27444434892 scopus 로고    scopus 로고
    • MetaSite: Understanding metabolism in human cytochromes from the perspective of the chemist
    • G. Cruciani MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist J. Med. Chem. 48 2005 6970 6979
    • (2005) J. Med. Chem. , vol.48 , pp. 6970-6979
    • Cruciani, G.1
  • 30
    • 17144398395 scopus 로고    scopus 로고
    • Anchor-GRIND: Filling the gap between standard 3D QSAR and the GRid-INdependent descriptors
    • F. Fontaine Anchor-GRIND: filling the gap between standard 3D QSAR and the GRid-INdependent descriptors J. Med. Chem. 48 2005 2687 2694
    • (2005) J. Med. Chem. , vol.48 , pp. 2687-2694
    • Fontaine, F.1
  • 31
    • 78650738986 scopus 로고    scopus 로고
    • MetaSite
    • MetaSite: http://www.moldiscovery.com/soft-metasite.php
  • 32
    • 77953322016 scopus 로고    scopus 로고
    • Site of metabolism prediction on cytochrome P450 2C9: A knowledge-based docking approach
    • A. Tarcsay Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach J. Comput.-Aided Mol. Des. 24 2010 399 408
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 399-408
    • Tarcsay, A.1
  • 33
    • 84880764388 scopus 로고    scopus 로고
    • Drug metabolism: Seeking the soft spots
    • P. Kirkpatrick Drug metabolism: seeking the soft spots Nature Rev. Drug Discov. 8 2009 196
    • (2009) Nature Rev. Drug Discov. , vol.8 , pp. 196
    • Kirkpatrick, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.