Computational docking simulations of a DNA-aptamer for argininamide and related ligands

From Cascaded Catalytic Nucleic Acids to Enzyme–DNA Nanostructures: Controlling Reactivity, Sensing, Logic Operations, and Assembly of Complex Structures

(2014) Fuan Wang et al.   CHEMICAL REVIEWS

An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates

(2014) C. S. Padlan et al.   RNA

Chemistry and formulations for siRNA therapeutics

(2013) Andrzej Gallas et al.   CHEMICAL SOCIETY REVIEWS

Prediction of noncovalent Drug/DNA interaction using computational docking models: Studies with over 1350 launched drugs

(2013) Ronald D. Snyder et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Docking Studies on DNA Intercalators

(2013) Yocheved Gilad et al.   Journal of Chemical Information and Modeling

Motion of transfer RNA from the A/T state into the A-site using docking and simulations

(2013) Thomas Caulfield et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular dynamics simulation of the induced-fit binding process of DNA aptamer andL-argininamide

(2012) Po-Hsun Lin et al.   Biotechnology Journal

Functionalized DNA Nanostructures

(2012) Ofer I. Wilner et al.   CHEMICAL REVIEWS

Benzothiadiazoles as DNA intercalators: Docking and simulation

(2012) Paulo Augusto Netz   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

A DNA Nanostructure Platform for Directed Assembly of Synthetic Vaccines

(2012) Xiaowei Liu et al.   NANO LETTERS

The Dynamic Nature of RNA as Key to Understanding Riboswitch Mechanisms

(2011) Andrea Haller et al.   ACCOUNTS OF CHEMICAL RESEARCH

Aptamer Modules as Sensors and Detectors

(2011) Michael Famulok et al.   ACCOUNTS OF CHEMICAL RESEARCH

Nucleic Acid Based Molecular Devices

(2011) Yamuna Krishnan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enantioselective CuII-Catalyzed Diels-Alder and Michael Addition Reactions in Water Using Bio-Inspired Triazacyclophane-Based Ligands

(2011) H. Bauke Albada et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

(2011) Andrew C Stelzer et al.   Nature Chemical Biology

Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine

(2011) Kirill A Afonin et al.   Nature Protocols

DNA nanomedicine: Engineering DNA as a polymer for therapeutic and diagnostic applications

(2010) Michael J. Campolongo et al.   ADVANCED DRUG DELIVERY REVIEWS

Binary Probes for Nucleic Acid Analysis

(2010) Dmitry M. Kolpashchikov   CHEMICAL REVIEWS

Functional nucleic acid nanostructures and DNA machines

(2010) Carsten Teller et al.   CURRENT OPINION IN BIOTECHNOLOGY

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

(2010) Simone Fulle et al.   Journal of Chemical Information and Modeling

Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations

(2010) Roman Reshetnikov et al.   Journal of Chemical Theory and Computation

Development of DNA aptamers using Cell-SELEX

(2010) Kwame Sefah et al.   Nature Protocols

The Chemical Biology of Aptamers

(2009) Günter Mayer   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular dynamics analysis of the wild type and dF508 mutant structures of the human CFTR–nucleotide binding domain 1

(2009) Paola Bisignano et al.   BIOCHIMIE

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Docking Studies on DNA-Ligand Interactions: Building and Application of a Protocol To Identify the Binding Mode

(2009) Clarisse G. Ricci et al.   Journal of Chemical Information and Modeling

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Thermodynamic basis of chiral recognition in a DNA aptamer

(2009) Po-Hsun Lin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Targeting RNA with Small Molecules

(2008) Jason R. Thomas et al.   CHEMICAL REVIEWS

Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets

(2008) Christophe Guilbert et al.   Journal of Chemical Information and Modeling

Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex

(2008) Patrick A. Holt et al.   Journal of Chemical Information and Modeling