메뉴 건너뛰기




Volumn 2, Issue 7, 2011, Pages 489-493

Target flexibility in RNA-ligand docking modeled by elastic potential grids

Author keywords

DrugScore; elasticity theory; flexible docking; RNA ligand interactions; structure based drug design

Indexed keywords

LIGAND; RNA;

EID: 79960431412     PISSN: None     EISSN: 19485875     Source Type: Journal    
DOI: 10.1021/ml100217h     Document Type: Article
Times cited : (23)

References (28)
  • 1
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. Engl. 2002, 41 (15) 2644-2676
    • (2002) Angew. Chem., Int. Ed. Engl. , vol.41 , Issue.15 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 3
    • 0030324870 scopus 로고    scopus 로고
    • A docking and modelling strategy for peptide-RNA complexes: Applications to BIV Tat-TAR and HIV Rev-RBE
    • Srinivasan, J.; Leclerc, F.; Xu, W.; Ellington, A. D.; Cedergren, R. A docking and modelling strategy for peptide-RNA complexes: Applications to BIV Tat-TAR and HIV Rev-RBE Fold Des. 1996, 1 (6) 463-472 (Pubitemid 126748242)
    • (1996) Folding and Design , vol.1 , Issue.6 , pp. 463-472
    • Srinivasan, J.1    Leclerc, F.2    Xu, W.3    Ellington, A.D.4    Cedergren, R.5
  • 4
    • 0031894779 scopus 로고    scopus 로고
    • Modeling RNA-ligand interactions: The Rev-binding element RNA- aminoglycoside complex
    • DOI 10.1021/jm970372r
    • Leclerc, F.; Cedergren, R. Modeling RNA-ligand interactions: The Rev-binding element RNA-aminoglycoside complex J. Med. Chem. 1998, 41 (2) 175-182 (Pubitemid 28114359)
    • (1998) Journal of Medicinal Chemistry , vol.41 , Issue.2 , pp. 175-182
    • Leclerc, F.1    Cedergren, R.2
  • 5
    • 0033535566 scopus 로고    scopus 로고
    • Docking of cationic antibiotics to negatively charged pockets in RNA folds
    • DOI 10.1021/jm981108g
    • Hermann, T.; Westhof, E. Docking of cationic antibiotics to negatively charged pockets in RNA folds J. Med. Chem. 1999, 42 (7) 1250-1261 (Pubitemid 29181147)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.7 , pp. 1250-1261
    • Hermann, T.1    Westhof, E.2
  • 6
    • 33646169319 scopus 로고    scopus 로고
    • Conformational dynamics of RNA-peptide binding: A molecular dynamics simulation study
    • Mu, Y.; Stock, G. Conformational dynamics of RNA-peptide binding: A molecular dynamics simulation study Biophys. J. 2006, 90 (2) 391-399
    • (2006) Biophys. J. , vol.90 , Issue.2 , pp. 391-399
    • Mu, Y.1    Stock, G.2
  • 7
    • 0030954877 scopus 로고    scopus 로고
    • Structure-based discovery of ligands targeted to the RNA double helix
    • DOI 10.1021/bi970756j
    • Chen, Q.; Shafer, R. H.; Kuntz, I. D. Structure-based discovery of ligands targeted to the RNA double helix Biochemistry 1997, 36 (38) 11402-11407 (Pubitemid 27408622)
    • (1997) Biochemistry , vol.36 , Issue.38 , pp. 11402-11407
    • Chen, Q.1    Shafer, R.H.2    Kuntz, I.D.3
  • 8
    • 1242272760 scopus 로고    scopus 로고
    • Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK
    • DOI 10.1002/bip.10541
    • Kang, X.; Shafer, R. H.; Kuntz, I. D. Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK Biopolymers 2004, 73 (2) 192-204 (Pubitemid 38220378)
    • (2004) Biopolymers , vol.73 , Issue.2 , pp. 192-204
    • Kang, X.1    Shafer, R.H.2    Kuntz, I.D.3
  • 9
    • 4043058000 scopus 로고    scopus 로고
    • Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®
    • DOI 10.1023/B:JCAM.0000035199.48747.1e
    • Morley, S. D.; Afshar, M. Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock J. Comput.-Aided Mol. Des. 2004, 18 (3) 189-208 (Pubitemid 39069414)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.3 , pp. 189-208
    • Morley, S.D.1    Afshar, M.2
  • 12
    • 76649139475 scopus 로고    scopus 로고
    • Molecular recognition of RNA: Challenges for modelling interactions and plasticity
    • Fulle, S.; Gohlke, H. Molecular recognition of RNA: Challenges for modelling interactions and plasticity J. Mol. Recognit. 2010, 23 (2) 220-231
    • (2010) J. Mol. Recognit. , vol.23 , Issue.2 , pp. 220-231
    • Fulle, S.1    Gohlke, H.2
  • 13
    • 35248883964 scopus 로고    scopus 로고
    • RNA - Knowledge-based scoring function to predict RNA - Ligand interactions
    • DOI 10.1021/ci700134p
    • Pfeffer, P.; Gohlke, H. DrugScoreRNA - knowledge-based scoring function to predict RNA-ligand interactions J. Chem. Inf. Model. 2007, 47 (5) 1868-1876 (Pubitemid 47561134)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.5 , pp. 1868-1876
    • Pfeffer, P.1    Gohlke, H.2
  • 14
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • DOI 10.1006/jmbi.1999.3371
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions J. Mol. Biol. 2000, 295 (2) 337-356 (Pubitemid 30045364)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.2 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 15
    • 44849090619 scopus 로고    scopus 로고
    • Analyzing the flexibility of RNA structures by constraint counting
    • Fulle, S.; Gohlke, H. Analyzing the flexibility of RNA structures by constraint counting Biophys. J. 2008, 94 (11) 4202-4219
    • (2008) Biophys. J. , vol.94 , Issue.11 , pp. 4202-4219
    • Fulle, S.1    Gohlke, H.2
  • 16
    • 79960435161 scopus 로고    scopus 로고
    • HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations
    • Fulle, S.; Christ, N. A.; Kestner, E.; Gohlke, H. HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations J. Chem. Inf. Model. 2010, 51, 6
    • (2010) J. Chem. Inf. Model. , vol.51 , pp. 6
    • Fulle, S.1    Christ, N.A.2    Kestner, E.3    Gohlke, H.4
  • 18
    • 33747891811 scopus 로고    scopus 로고
    • The ribosomal A-site as an inspiration for the design of RNA binders
    • Tor, Y. The ribosomal A-site as an inspiration for the design of RNA binders Biochimie 2006, 88 (8) 1045-1051
    • (2006) Biochimie , vol.88 , Issue.8 , pp. 1045-1051
    • Tor, Y.1
  • 19
    • 0026651395 scopus 로고
    • Conformation of the TAR RNA-arginine complex by NMR spectroscopy
    • Puglisi, J. D.; Tan, R.; Calnan, B. J.; Frankel, A. D.; Williamson, J. R. Conformation of the TAR RNA-arginine complex by NMR spectroscopy Science 1992, 257 (5066) 76-80
    • (1992) Science , vol.257 , Issue.5066 , pp. 76-80
    • Puglisi, J.D.1    Tan, R.2    Calnan, B.J.3    Frankel, A.D.4    Williamson, J.R.5
  • 20
    • 0034671676 scopus 로고    scopus 로고
    • Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide
    • Nifosi, R.; Reyes, C. M.; Kollman, P. A. Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide Nucleic Acids Res. 2000, 28 (24) 4944-4955 (Pubitemid 32014265)
    • (2000) Nucleic Acids Research , vol.28 , Issue.24 , pp. 4944-4955
    • Nifosi, R.1    Reyes, C.M.2    Kollman, P.A.3
  • 21
    • 47349127321 scopus 로고    scopus 로고
    • Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets
    • Guilbert, C.; James, T. L. Docking to RNA via root-mean-square-deviation- driven energy minimization with flexible ligands and flexible targets J. Chem. Inf. Model. 2008, 48 (6) 1257-1268
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.6 , pp. 1257-1268
    • Guilbert, C.1    James, T.L.2
  • 22
    • 32344449937 scopus 로고    scopus 로고
    • Docking of aminoglycosides to hydrated and flexible RNA
    • DOI 10.1021/jm0508437
    • Moitessier, N.; Westhof, E.; Hanessian, S. Docking of aminoglycosides to hydrated and flexible RNA J. Med. Chem. 2006, 49 (3) 1023-1033 (Pubitemid 43221650)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.3 , pp. 1023-1033
    • Moitessier, N.1    Westhof, E.2    Hanessian, S.3
  • 23
    • 68149149959 scopus 로고    scopus 로고
    • Elastic potential grids: Accurate and efficient representation of intermolecular interactions for fully flexible docking
    • Kazemi, S.; Krueger, D. M.; Sirockin, F.; Gohlke, H. Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking ChemMedChem 2009, 4 (8) 1264-1268
    • (2009) ChemMedChem , vol.4 , Issue.8 , pp. 1264-1268
    • Kazemi, S.1    Krueger, D.M.2    Sirockin, F.3    Gohlke, H.4
  • 27
    • 33947716119 scopus 로고    scopus 로고
    • Software news and update a semiempirical free energy force field with charge-based desolvation
    • DOI 10.1002/jcc.20634
    • Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A semiempirical free energy force field with charge-based desolvation J. Comput. Chem. 2007, 28 (6) 1145-1152 (Pubitemid 46506716)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.6 , pp. 1145-1152
    • Huey, R.1    Morris, G.M.2    Olson, A.J.3    Goodsell, D.S.4
  • 28


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.