메뉴 건너뛰기




Volumn 46, Issue 5, 2006, Pages 2071-2084

Noise reduction method for molecular interaction energy: Application to in silico drug screening and in silico target protein screening

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; DATABASE SYSTEMS; FREE ENERGY; LEARNING SYSTEMS; MATRIX ALGEBRA; NOISE ABATEMENT; PROTEINS; TARGETS;

EID: 33750303121     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci060152z     Document Type: Article
Times cited : (33)

References (36)
  • 2
    • 24644481912 scopus 로고    scopus 로고
    • Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models
    • Cotesta, S.; Giordanetto, F.; Trosset, J.-Y.; Crivori, P.; Kroemer, R. T.; Stouten, P. F. W.; Vulpetti, A.Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. Proteins 2005, 60, 629-643.
    • (2005) Proteins , vol.60 , pp. 629-643
    • Cotesta, S.1    Giordanetto, F.2    Trosset, J.-Y.3    Crivori, P.4    Kroemer, R.T.5    Stouten, P.F.W.6    Vulpetti, A.7
  • 3
    • 6344294057 scopus 로고    scopus 로고
    • FlexX-Scan: Fast, structure-based virtual screening
    • Schellhammer, I.; Rarey, M. FlexX-Scan: Fast, structure-based virtual screening. Proteins 2004, 57, 504-517.
    • (2004) Proteins , vol.57 , pp. 504-517
    • Schellhammer, I.1    Rarey, M.2
  • 4
    • 23944454816 scopus 로고    scopus 로고
    • Virtual screening of biogenic amine-binding g-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols
    • Evers, A.; Hessler, G.; Matter, H.; Klabunde, T. Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols. J. Med. Chem. 2005, 48, 5448-5465.
    • (2005) J. Med. Chem. , vol.48 , pp. 5448-5465
    • Evers, A.1    Hessler, G.2    Matter, H.3    Klabunde, T.4
  • 5
    • 11144237579 scopus 로고    scopus 로고
    • A novel class of inhibitors of peptide deformylase discovered through high-throughput screening and virtual ligand screening
    • Howard, M. H.; Cenizal, T.; Gutteridge, S.; Hanna, W. S.; Tao, Y.; Totrov, M.; Wittenbach, V. A.; Zheng, Y.-J. A Novel Class of Inhibitors of Peptide Deformylase Discovered through High-Throughput Screening and Virtual Ligand Screening. J. Med. Chem. 2004, 47, 6669-6672.
    • (2004) J. Med. Chem. , vol.47 , pp. 6669-6672
    • Howard, M.H.1    Cenizal, T.2    Gutteridge, S.3    Hanna, W.S.4    Tao, Y.5    Totrov, M.6    Wittenbach, V.A.7    Zheng, Y.-J.8
  • 6
    • 7444270927 scopus 로고    scopus 로고
    • POT-DMC: A virtual screening method for the identification of potent hits
    • Godden, J. W.; Stahura, F. L.; Bajorath, J. POT-DMC: A Virtual Screening Method for the Identification of Potent Hits. J. Med. Chem. 2004, 47, 5608-5611
    • (2004) J. Med. Chem. , vol.47 , pp. 5608-5611
    • Godden, J.W.1    Stahura, F.L.2    Bajorath, J.3
  • 7
    • 18644371468 scopus 로고    scopus 로고
    • β- selective ligands as potential preventative therapy against age-related neurodegenerative diseases
    • β-Selective Ligands as Potential Preventative Therapy against Age-Related Neurodegenerative Diseases. J. Med. Chem. 2005, 48, 3463-3466
    • (2005) J. Med. Chem. , vol.48 , pp. 3463-3466
    • Zhao, L.1    Brinton, R.D.2
  • 8
    • 0041342061 scopus 로고    scopus 로고
    • Identification of "latent hits" in compound screening collections
    • Mestres, J.; Veeneman, G. H. Identification of "Latent Hits" in Compound Screening Collections, J. Med. Chem. 2003, 46, 3441-3444.
    • (2003) J. Med. Chem. , vol.46 , pp. 3441-3444
    • Mestres, J.1    Veeneman, G.H.2
  • 10
    • 0037963157 scopus 로고    scopus 로고
    • Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors
    • Cavasotto, C. N.; Orry, A. J. W.; Abagyan, R. A. Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors. Proteins 2003, 51, 423-433.
    • (2003) Proteins , vol.51 , pp. 423-433
    • Cavasotto, C.N.1    Orry, A.J.W.2    Abagyan, R.A.3
  • 11
    • 14044270215 scopus 로고    scopus 로고
    • Structure basis for a broad but selective ligand spectrum of a mouse olfactory receptor: Mapping the odorant-binding site
    • Katada, S.; Hirokawa, T.; Oka, Y.; Suwa, M.; Touhara, K. Structure basis for a broad but selective ligand spectrum of a mouse olfactory receptor: mapping the odorant-binding site. J. Neurosci. 2005, 25, 1806-1815.
    • (2005) J. Neurosci. , vol.25 , pp. 1806-1815
    • Katada, S.1    Hirokawa, T.2    Oka, Y.3    Suwa, M.4    Touhara, K.5
  • 13
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 14
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willet, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 15
    • 0036606204 scopus 로고    scopus 로고
    • ConsDock: A new program for the consensus analysis of protein-ligand interactions
    • Paul, N.; Rognan, D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins 2002, 47, 521-533.
    • (2002) Proteins , vol.47 , pp. 521-533
    • Paul, N.1    Rognan, D.2
  • 16
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using tabu search and an empirical estimate of binding affinity
    • Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 1998, 33, 367-382.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Clark, D.E.3    Westhead, D.R.4    Eldridge, M.D.5
  • 18
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D. S.; Olson, A. J. Automated Docking of Substrates to Proteins by Simulated Annealing, Proteins 1990, 8, 195-202.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 19
    • 0034332970 scopus 로고    scopus 로고
    • DARWIN: A program for docking flexible molecules
    • Taylor, J. S.; Burnett, R. M. DARWIN: A program for docking flexible molecules. Proteins 2000, 41, 173-191.
    • (2000) Proteins , vol.41 , pp. 173-191
    • Taylor, J.S.1    Burnett, R.M.2
  • 20
    • 84986522918 scopus 로고
    • ICM: A new method for structure modeling and design: Application to docking and structure prediction from the disordered native conformation
    • Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM: a new method for structure modeling and design: application to docking and structure prediction from the disordered native conformation. J. Comput. Chem. 1994, 15, 488-506.
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 21
    • 0028584446 scopus 로고
    • Structure-based drug design
    • Colman, P. M.Structure-based drug design. Curr. Opin. Struct. Biol. 1994, 4, 868-874.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 868-874
    • Colman, P.M.1
  • 23
    • 24944576105 scopus 로고    scopus 로고
    • Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening
    • Fukunishi, Y.; Mikami, Y.; Nakamura, H. Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graphics Modell. 2005, 24, 34-45.
    • (2005) J. Mol. Graphics Modell. , vol.24 , pp. 34-45
    • Fukunishi, Y.1    Mikami, Y.2    Nakamura, H.3
  • 24
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 2005, 48, 2325-2335.
    • (2005) J. Med. Chem. , vol.48 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 25
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 26
    • 0346731233 scopus 로고    scopus 로고
    • Multiple active site corrections for docking and virtual screening
    • Vigers, G. P. A.; Rizzi, J. P. Multiple active site corrections for docking and virtual screening. J. Med. Chem. 2004, 47, 80-89.
    • (2004) J. Med. Chem. , vol.47 , pp. 80-89
    • Vigers, G.P.A.1    Rizzi, J.P.2
  • 27
    • 33748594188 scopus 로고    scopus 로고
    • Multiple target screening method for robust and accurate in silico ligand screening
    • Fukunishi, Y.; Mikami, Y.; Kubota, S.; Nakamura, H. Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graphics Modell. 2005, 25, 61-70.
    • (2005) J. Mol. Graphics Modell. , vol.25 , pp. 61-70
    • Fukunishi, Y.1    Mikami, Y.2    Kubota, S.3    Nakamura, H.4
  • 28
    • 31544477769 scopus 로고    scopus 로고
    • Classification of chemical compounds by protein-compound docking for use in designing a focused library
    • Fukunishi, Y.; Mikami, Y.; Takedomi, K.; Yamanouchi, M.; Shima, H.; Nakamura, H. Classification of chemical compounds by protein-compound docking for use in designing a focused library. J. Med. Chem. 2006, 49, 523-533.
    • (2006) J. Med. Chem. , vol.49 , pp. 523-533
    • Fukunishi, Y.1    Mikami, Y.2    Takedomi, K.3    Yamanouchi, M.4    Shima, H.5    Nakamura, H.6
  • 31
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges
    • Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 32
    • 0000125764 scopus 로고
    • A new model for calculating atomic charges in molecules
    • Gasteiger, J.; Marsili, M. A new model for calculating atomic charges in molecules. Tetrahedron Lett. 1978, 3181-3184.
    • (1978) Tetrahedron Lett. , pp. 3181-3184
    • Gasteiger, J.1    Marsili, M.2
  • 34
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.