Flexibility databases | Protein structure data analysis

Provides access to information about mechanical stretching of biomolecules. BSDB provides information about expected values of Fmax for, about 17 134 proteins. The values and other characteristics of the unfolding process, including the nature of identified mechanical clamps, are available. Two calculated force, F, versus displacement, d, curves are also displayed. The database relates to four external databases: PDB, CATH, SCOP and Gene Ontology database.

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.

The purpose of this database is to represent the relationship between protein structural change and ligand binding.

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.

A large library of molecular dynamics trajectories of representative protein structures, prepared with the state-of-the-art technology. Basic analyses and trajectories stripped of solvent molecules at a reduced resolution level are available from MoDEL.