☆ 4.7 Article

Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Automated Docking Screens: A Feasibility Study

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JOURNAL OF MEDICINAL CHEMISTRY (2009)

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Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

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NATURE STRUCTURAL & MOLECULAR BIOLOGY (2009)

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Review Biochemical Research Methods

A short guide for molecular dynamics simulations of RNA systems

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METHODS (2009)

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Article Multidisciplinary Sciences

A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding

Jonathan F. Arambula et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

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Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression

Elaine R. Lee et al.

RNA BIOLOGY (2009)

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Article Biochemistry & Molecular Biology

DOCK 6: Combining techniques to model RNA-small molecule complexes

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RNA (2009)

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Review Chemistry, Multidisciplinary

Targeting RNA with small molecules

Jason R. Thomas et al.

CHEMICAL REVIEWS (2008)

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Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets

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JOURNAL OF CHEMICAL INFORMATION AND MODELING (2008)

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Article Chemistry, Multidisciplinary

Dynamic Combinatorial Selection of Molecules Capable of Inhibiting the (CUG) Repeat RNA-MBNL1 Interaction In Vitro: Discovery of Lead Compounds Targeting Myotonic Dystrophy (DM1)

Peter C. Gareiss et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)

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Article Chemistry, Medicinal

DrugScoreRNA -: Knowledge-based scoring function to predict RNA-ligand interactions

Patrick Pfeffer et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

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Review Multidisciplinary Sciences

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Ewan Birney et al.

NATURE (2007)

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Article Biochemistry & Molecular Biology

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain

Adam Roth et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2007)

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Article Chemistry, Medicinal

Benchmarking sets for molecular docking

Niu Huang et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

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Article Biochemistry & Molecular Biology

Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition

Thomas E. Edwards et al.

STRUCTURE (2006)

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Article Multidisciplinary Sciences

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

Alexander Serganov et al.

NATURE (2006)

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MeRNA: a database of metal ion binding sites in RNA structures

Liliana R. Stefan et al.

NUCLEIC ACIDS RESEARCH (2006)

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MODOMICS: a database of RNA modification pathways

Stanislaw Dunin-Horkawicz et al.

NUCLEIC ACIDS RESEARCH (2006)

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Molecular-recognition characteristics of SAM-binding riboswitches

J Lim et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2006)

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Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding

B Francois et al.

NUCLEIC ACIDS RESEARCH (2005)

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Article Chemistry, Medicinal

Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

TA Halgren et al.

JOURNAL OF MEDICINAL CHEMISTRY (2004)

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Article Biochemistry & Molecular Biology

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

SD Morley et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2004)

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Structure-based drug design targeting an inactive RNA conformation: Exploiting the flexibility of HIV-1 TAR RNA

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Rational design of inhibitors of HIV-1 TAR RNA through the stabilisation of electrostatic hot spots

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Review Chemistry, Medicinal

Validation of automated docking programs for docking and database screening against RNA drug targets

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JOURNAL OF MEDICINAL CHEMISTRY (2004)

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Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

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CHEMISTRY & BIOLOGY (2004)

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Adenine riboswitches and gene activation by disruption of a transcription terminator

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NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)

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Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening

ZH Du et al.

CHEMISTRY & BIOLOGY (2002)

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Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR

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Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

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The Protein Data Bank

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