DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA-Ligand Interactions
暂无分享,去创建一个
[1] Gerhard Klebe,et al. Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. , 2002, Journal of medicinal chemistry.
[2] D. Patel,et al. Adaptive recognition by nucleic acid aptamers. , 2000, Science.
[3] Thomas Hermann,et al. Drugs targeting the ribosome. , 2005, Current opinion in structural biology.
[4] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[5] D. N. Tarasov,et al. A novel scoring function for molecular docking , 2003, J. Comput. Aided Mol. Des..
[6] G. Varani,et al. Targeting RNA with small-molecule drugs: therapeutic promise and chemical challenges. , 2001, Accounts of chemical research.
[7] Martin Karplus,et al. MCSS-based predictions of RNA binding sites , 1999 .
[8] H. Gohlke,et al. Improving binding mode predictions by docking into protein-specifically adapted potential fields. , 2005, Journal of medicinal chemistry.
[9] J. Puglisi,et al. Structural origins of gentamicin antibiotic action , 1998, The EMBO journal.
[10] G. Schneider,et al. New Inhibitors of the Tat–TAR RNA Interaction Found with a “Fuzzy” Pharmacophore Model , 2005, Chembiochem : a European journal of chemical biology.
[11] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[12] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[13] A. Cheng,et al. Design of RNA-binding proteins and ligands. , 2001, Current opinion in structural biology.
[14] Irwin D Kuntz,et al. Calculation of ligand‐nucleic acid binding free energies with the generalized‐born model in DOCK , 2004, Biopolymers.
[15] Hongyi Zhou,et al. An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state , 2004, Protein science : a publication of the Protein Society.
[16] Gabriele Varani,et al. Validation of automated docking programs for docking and database screening against RNA drug targets. , 2004, Journal of medicinal chemistry.
[17] Pedro Alexandrino Fernandes,et al. Protein–ligand docking: Current status and future challenges , 2006, Proteins.
[18] Song Liu,et al. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. , 2005, Journal of medicinal chemistry.
[19] Gerhard Klebe,et al. Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function , 2000 .
[20] Gerhard Stock,et al. Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study. , 2006, Biophysical journal.
[21] A D Ellington,et al. A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV Rev-RBE. , 1996, Folding & design.
[22] S. David Morley,et al. Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock® , 2004, J. Comput. Aided Mol. Des..
[23] T. Hermann,et al. Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes. , 2000, Angewandte Chemie.
[24] T. Hermann,et al. RNA as a target for small-molecule therapeutics , 2005 .
[25] Daniel N. Wilson,et al. Protein synthesis and ribosome structure : translating the genome , 2004 .
[26] A. Gatignol,et al. HIV-1 TAR RNA: the target of molecular interactions between the virus and its host. , 2005, Current HIV research.
[27] G. Klebe,et al. Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.
[28] C. Wong,et al. RNA as a target for small molecules. , 2000, Current opinion in chemical biology.
[29] Fenglou Mao,et al. Potential of mean force for protein–protein interaction studies , 2002, Proteins.
[30] Hongyi Zhou,et al. The dependence of all-atom statistical potentials on structural training database. , 2004, Biophysical journal.
[31] W Patrick Walters,et al. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.
[32] D. J. Price,et al. Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.
[33] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[34] Janet M. Thornton,et al. BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential , 1999 .
[35] Brian K. Shoichet,et al. Virtual screening of chemical libraries , 2004, Nature.
[36] E Westhof,et al. Docking of cationic antibiotics to negatively charged pockets in RNA folds. , 1999, Journal of medicinal chemistry.
[37] Ruben Abagyan,et al. Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR , 2000, J. Comput. Aided Mol. Des..
[38] Ming Yang. Discoveries of Tat-TAR interaction inhibitors for HIV-1. , 2005, Current drug targets. Infectious disorders.
[39] Shaomeng Wang,et al. M-score: a knowledge-based potential scoring function accounting for protein atom mobility. , 2006, Journal of medicinal chemistry.
[40] Djamal Bouzida,et al. Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective. , 2002, Current opinion in structural biology.
[41] Grant R. Zimmermann,et al. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA , 1997, Nature Structural Biology.
[42] A. M. Ruvinsky,et al. The key role of atom types, reference states, and interaction cutoff radii in the knowledge‐based method: New variational approach , 2005, Proteins.
[43] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[44] D. Haussler,et al. The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome , 2004, PLoS biology.
[45] I. Muegge. PMF scoring revisited. , 2006, Journal of medicinal chemistry.
[46] Stephen Hanessian,et al. Docking of aminoglycosides to hydrated and flexible RNA. , 2006, Journal of medicinal chemistry.
[47] G. Klebe,et al. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors , 2002 .
[48] Renxiao Wang,et al. Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.
[49] G. Klebe,et al. Statistical potentials and scoring functions applied to protein-ligand binding. , 2001, Current opinion in structural biology.
[50] I D Kuntz,et al. Structure-based discovery of ligands targeted to the RNA double helix. , 1997, Biochemistry.
[51] R Cedergren,et al. Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex. , 1998, Journal of medicinal chemistry.
[52] M. V. Subbotin,et al. PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB , 2004, J. Comput. Aided Mol. Des..
[53] R. Nussinov,et al. Folding funnels, binding funnels, and protein function , 1999, Protein science : a publication of the Protein Society.
[54] G. Klebe,et al. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. , 2005, Journal of medicinal chemistry.
[55] R. Rando,et al. A high-throughput fluorescence screen to monitor the specific binding of antagonists to RNA targets. , 1998, Analytical biochemistry.
[56] R. Griffey,et al. Multiplexed screening of neutral mass-tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: a paradigm for high-throughput affinity screening. , 1999, Analytical chemistry.
[57] J. Gasteiger,et al. ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .
[58] R. Griffey,et al. Determinants of aminoglycoside-binding specificity for rRNA by using mass spectrometry. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[59] Zhihua Du,et al. Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. , 2002, Chemistry & biology.
[60] Gennady M Verkhivker,et al. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. , 2003, Physical review letters.