Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres.
Curves+ is a revised version of the Curves approach for analysing the structure of nucleic acids.
DNAlive. DNAlive is a tool for the analysis and graphical display of structural and physical characteristics of genomic DNA. The web server implements a wide repertoire of metrics to derive physical information from DNA sequences with a powerful interface to derive 3D information on large sequences of both naked and protein-bound DNAs.
FlexServ. Web portal for the analysis of flexibility including the generation of coarse-grained molecular dynamics trajectories, analysis of essential dynamics, BFactors, hinge points and flexibility correlations.
GOdMD is a new algorithm to trace conformational transitions in proteins. The method uses discrete molecular dynamics as engine to sample protein conformational space. A multiple minima Go-like potential energy function is used in combination with several enhancing sampling strategies, such as metadynamics, Maxwell-Demon molecular dynamics, and essential dynamics.
MDdMD is a new method for determining pathways for conformational transitions in macromolecules based on the use of discrete molecular dynamics and biasing techniques based on a combination of essential dynamics and Maxwell-Demon sampling techniques.
MDWeb & MDMoby. A comprehensive set of tools to allow automated setup and analysis of molecular dynamics trajectories. Access is available through a Web portal, but also through a series of web-services developed in the Biomoby framework.
MoDEL (Molecular Dynamics Extended Library) is a database holding over 1,800 trajectories ranging from 10 ns to 1ms in length, from a representative set of protein structures.
NAFlex (Nucleic Acid Flexibility). Web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server offers a variety of methods to explore nucleic acid flexibility, from coarse-grained low resolution mesoscopic models to atomistic molecular dynamics simulations.
