RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs

Hybrid simulation approach incorporating microscopic interaction along with rigid body degrees of freedom for stacking between base pairs

(2016) Manas Mondal et al.   BIOPOLYMERS

RNABP COGEST: a resource for investigating functional RNAs

(2015) Sohini Bhattacharya et al.   Database-The Journal of Biological Databases and Curation

Twenty-five years of nucleic acid simulations

(2013) Thomas E. Cheatham et al.   BIOPOLYMERS

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

(2013) A. I. Petrov et al.   RNA

Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding

(2012) Sankar Basu et al.   BIOPHYSICAL JOURNAL

Structure and Energy of Non-Canonical Basepairs: Comparison of Various Computational Chemistry Methods with Crystallographic Ensembles

(2012) Swati Panigrahi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structural Variations of Single and Tandem Mismatches in RNA Duplexes: A Joint MD Simulation and Crystal Structure Database Analysis

(2012) Sukanya Halder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

HD-RNAS: An Automated Hierarchical Database of RNA Structures

(2012) Shubhra Sankar Ray et al.   Frontiers in Genetics

Nucleosome Structure(s) and Stability: Variations on a Theme

(2011) Andrew J. Andrews et al.   Annual Review of Biophysics

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

(2011) C. Blanchet et al.   NUCLEIC ACIDS RESEARCH

Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA

(2010) Sukanya Halder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Insight into the Sequence Dependence of Nucleosome Positioning

(2010) Bin Wu et al.   STRUCTURE

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

(2009) Dong Xu et al.   PLoS One

The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols