Conformational diversity databases | Protein structure data analysis
In many biological processes, proteins have important interactions with various molecules such as proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions.
A proteome-scale database of conformational transitions in proteins. TransAtlas web interface allows to browse the resulting database, search for a particular protein, visualize the conformational transition, and work with (or download) the intermediate atomistic structures generated. TransAtlas is part of the Integrated Platform for macromolecular flexibility: FlexPortal.
Classifies the helix-cappings or caps compiled from protein structures. The caps which was extracted have been classified according to geometry and conformation. They are organized and classified in a tree-like hierarchy. To each classification corresponding a level which concerns properties of the caps. This database allows user to browse protein data but also to upload and analyze sequence.
Contains incorrect conformations to improve protein structure prediction. Decoy ‘R’ Us provides a resource that allows scoring functions to be improved. It can be used to evaluate and improve scoring function performance for predicting structure, to elucidate the physical nature of protein–protein interactions or to assess the degree to which biologically relevant functional sites are preserved in predicted structures.
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.
Provides comprehensive information and a sophisticated interface for exploring conformational changes in proteins and their possible causes. All information is visualized in a unified and well-aligned manner, which is critical for capturing the relevance of different biological features. Possible applications of CCProf include analyses of protein disorder, secondary structure transition, protein flexibility/plasticity, protein interaction, post-translational modification and molecular dynamics. The update script of CCProf is executed weekly. The CCProf contains 986 187 protein structure pairs for 3123 proteins. In addition, CCProf provides a 3D view in which users can see the protein structures before and after conformational changes as well as binding targets that induce conformational changes.
Assists users for displaying the conformational angles in varied regions. CADB is an online repository that permits researchers to observe the details of amino-acids that lie in all three allowed and disallowed regions of the Ramachandran plot. Precisely, the conformation angles of any amino-acid residue from several protein structures in a particular secondary structural element can be displayed with the 3.0 version this database.
A database of proteins showing conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structures could be considered as different instances of protein dynamism. As a measure of the conformational diversity we use the maximum RMSD obtained comparing the structures deposited for each domain. The redundant structures were extracted following CATH structural classification and cross linked with additional information. In this way it is possible to relate a given amount of conformational diversity with different levels of information, such as protein function, presence of ligands and mutations, structural classification, active site information and organism taxonomy among others.