Allows users to make structural analysis. MolMovDB consists of a set of coupled hypertext pages with graphic images and a simple query box. It offers a lot of tools to systematize all instances of protein and nucleic acid movement.
Hosts a database of output files obtained from running Gaussian network model (GNM) calculations on Protein Data Bank (PDB) files and the means for visualizing these files in both 2-D and 3-D. iGNM 2.0 covers more than 95% of the structures currently available in the PDB. Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.
Contains simulations of representatives of essentially all known protein folds. The database provides an organizing framework, a repository, and a variety of access interfaces for the simulation and analysis data. Simulations of fold representatives are organized by their CDD definition. The SNP targets are further organized around the amino acid replacements involved and their related diseases. Coordinate and analysis data are loaded into the database and linked to their respective consensus domains.
A collection of redundant crystallographic structures for a given protein extensively linked with structural, biological and physicochemical information. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function.