BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations: Fig. 1.

(2015) Rajendra Kumar et al.   BIOINFORMATICS

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

(2014) Julien C. Thibault et al.   Journal of Chemical Information and Modeling

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

(2014) Marco Pasi et al.   NUCLEIC ACIDS RESEARCH

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

(2014) Julien C Thibault et al.   Journal of Cheminformatics

iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment

(2013) Julien C. Thibault et al.   Journal of Chemical Information and Modeling

NAFlex: a web server for the study of nucleic acid flexibility

(2013) Adam Hospital et al.   NUCLEIC ACIDS RESEARCH

The Nucleic Acid Database: new features and capabilities

(2013) Buvaneswari Coimbatore Narayanan et al.   NUCLEIC ACIDS RESEARCH

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations

(2012) Adam Hospital et al.   BIOINFORMATICS

Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function

(2012) Ulf Hensen et al.   PLoS One

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Dynameomics: A Comprehensive Database of Protein Dynamics

(2010) Marc W. van der Kamp et al.   STRUCTURE

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

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

Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data

(2008) C. Kehl et al.   PROTEIN ENGINEERING DESIGN & SELECTION