Flexibility databases | Protein structure data analysis

Consists of rotamer frequencies and their mean dihedral angles and variances as a function of the backbone dihedral angles. Rotamer Libraries has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances. It has a number of useful characteristics that will make it useful in a variety of applications in protein structure determination, prediction, and design.

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 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.

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.

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.

Explores the intrinsic flexibility of protein structures by analyzing structural variations between different depositions and chains in asymmetric unit of the same protein in PDB. PDBFlex allows to easily identify regions and types of structural flexibility present in a protein of interest. Structures of protein chains with identical sequences (sequence identity > 95%) were aligned, superimposed and clustered. Then global and local structural differences were calculated within these clusters. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.