Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

[1]  Harry F. Noller,et al.  Interaction of antibiotics with functional sites in 16S ribosomal RNA , 1987, Nature.

[2]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[3]  Paul R. Gerber,et al.  MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry , 1995, J. Comput. Aided Mol. Des..

[4]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[5]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[6]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[7]  B. Shoichet,et al.  Flexible ligand docking using conformational ensembles , 1998, Protein science : a publication of the Protein Society.

[8]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[9]  Hermann Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes. , 2000, Angewandte Chemie.

[10]  G. Klebe,et al.  Statistical potentials and scoring functions applied to protein-ligand binding. , 2001, Current opinion in structural biology.

[11]  Zhihua Du,et al.  Structure-based computational database screening, in vitro assay, and NMR assessment of compounds that target TAR RNA. , 2002, Chemistry & biology.

[12]  B. Matthews,et al.  A model binding site for testing scoring functions in molecular docking. , 2002, Journal of molecular biology.

[13]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[14]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[15]  R. Breaker,et al.  Adenine riboswitches and gene activation by disruption of a transcription terminator , 2004, Nature Structural &Molecular Biology.

[16]  R. Montange,et al.  Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine , 2004, Nature.

[17]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[18]  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..

[19]  Irwin D Kuntz,et al.  Calculation of ligand‐nucleic acid binding free energies with the generalized‐born model in DOCK , 2004, Biopolymers.

[20]  Richard D. Taylor,et al.  Virtual Screening Using Protein—Ligand Docking: Avoiding Artificial Enrichment. , 2004 .

[21]  Ajay N. Jain,et al.  Ligand-based structural hypotheses for virtual screening. , 2004, Journal of medicinal chemistry.

[22]  Gabriele Varani,et al.  Validation of automated docking programs for docking and database screening against RNA drug targets. , 2004, Journal of medicinal chemistry.

[23]  A. W. Schüttelkopf,et al.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.

[24]  Stephen R Holbrook,et al.  RNA structure: the long and the short of it , 2005, Current Opinion in Structural Biology.

[25]  R. Copeland,et al.  Fluorescence Polarization Method To Characterize Macrolide-Ribosome Interactions , 2005, Antimicrobial Agents and Chemotherapy.

[26]  Stephen Hanessian,et al.  Docking of aminoglycosides to hydrated and flexible RNA. , 2006, Journal of medicinal chemistry.

[27]  D. Lilley,et al.  Folding of the adenine riboswitch. , 2006, Chemistry & biology.

[28]  G. Klebe Virtual ligand screening: strategies, perspectives and limitations , 2006, Drug Discovery Today.

[29]  Lihe Zhang,et al.  Parametrization of a specific free energy function for automated docking against RNA targets using neural networks , 2006 .

[30]  Erin M Duffy,et al.  Structure-based drug design meets the ribosome. , 2006, Biochemical pharmacology.

[31]  R. Breaker,et al.  Riboswitches as antibacterial drug targets , 2006, Nature Biotechnology.

[32]  R. Batey,et al.  Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. , 2006, Journal of molecular biology.

[33]  B. Shoichet,et al.  Probing molecular docking in a charged model binding site. , 2006, Journal of molecular biology.

[34]  R. Batey,et al.  Modified pyrimidines specifically bind the purine riboswitch. , 2006, Journal of the American Chemical Society.

[35]  Ricardo L Mancera Molecular modeling of hydration in drug design. , 2007, Current opinion in drug discovery & development.

[36]  H. Schwalbe,et al.  Structures of RNA switches: insight into molecular recognition and tertiary structure. , 2007, Angewandte Chemie.

[37]  Holger Gohlke,et al.  DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA-Ligand Interactions , 2007, J. Chem. Inf. Model..

[38]  Daniel James,et al.  Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases , 2007, ChemMedChem.

[39]  Paul J Hergenrother,et al.  Targeting RNA with small molecules. , 2008, Chemical reviews.

[40]  So-Jung Park,et al.  Identification of novel ligands for the RNA pseudoknot that regulate −1 ribosomal frameshifting , 2008, Bioorganic & Medicinal Chemistry.

[41]  Amiram Goldblum,et al.  High quality binding modes in docking ligands to proteins , 2008, Proteins.

[42]  Thomas L. James,et al.  Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets , 2008, J. Chem. Inf. Model..

[43]  Andrea L Edwards,et al.  Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. , 2009, Structure.

[44]  F. Aboul-Ela,et al.  Design and implementation of an ribonucleic acid (RNA) directed fragment library. , 2009, Journal of medicinal chemistry.

[45]  Nicolas Moitessier,et al.  Docking Ligands into Flexible and Solvated Macromolecules. 4. Are Popular Scoring Functions Accurate for this Class of Proteins? , 2009, J. Chem. Inf. Model..

[46]  Ronald R. Breaker,et al.  Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression , 2009, RNA biology.

[47]  Marc C. Nicklaus,et al.  Comparison of Nine Programs Predicting pKa Values of Pharmaceutical Substances , 2009, J. Chem. Inf. Model..

[48]  M. Mack,et al.  The RFN riboswitch of Bacillus subtilis is a target for the antibiotic roseoflavin produced by Streptomyces davawensis , 2009, RNA biology.

[49]  I. Kuntz,et al.  DOCK 6: combining techniques to model RNA-small molecule complexes. , 2009, RNA.

[50]  R. Breaker,et al.  Design and antimicrobial action of purine analogues that bind Guanine riboswitches. , 2009, ACS chemical biology.

[51]  Ian H. Gilbert,et al.  One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening , 2009, Journal of medicinal chemistry.

[52]  Peter Kolb,et al.  Docking screens: right for the right reasons? , 2009, Current topics in medicinal chemistry.

[53]  Zhihai Liu,et al.  Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes , 2010, J. Comput. Chem..

[54]  Chris Oostenbrink,et al.  Improved ligand-protein binding affinity predictions using multiple binding modes. , 2010, Biophysical journal.

[55]  John Manchester,et al.  Evaluation of pKa Estimation Methods on 211 Druglike Compounds , 2010, J. Chem. Inf. Model..

[56]  Holger Gohlke,et al.  Molecular recognition of RNA: challenges for modelling interactions and plasticity , 2009, Journal of molecular recognition : JMR.

[57]  C. Abell,et al.  A fragment-based approach to identifying ligands for riboswitches. , 2010, ACS chemical biology.

[58]  Gisbert Schneider,et al.  Virtual screening: an endless staircase? , 2010, Nature Reviews Drug Discovery.

[59]  Jie Shen,et al.  Accuracy Assessment of Protein-Based Docking Programs against RNA Targets , 2010, J. Chem. Inf. Model..

[60]  A. Serganov Determination of riboswitch structures: Light at the end of the tunnel? , 2010, RNA biology.

[61]  Antti Poso,et al.  The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening. , 2010 .

[62]  D. Lafontaine,et al.  Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine-Related Metabolic Pathways , 2010, PLoS pathogens.

[63]  Markus A. Lill,et al.  A Medicinal Chemist's Guide to Molecular Interactions , 2013 .