A database of pairwise, structure-based alignments for structurally analogous motifs in proteins. Applications of this database may range from protein evolution studies, e.g. development of remote homology inference tools and discriminators between homologs and analogs, to protein-folding research, since in the absence of evolutionary reasons, similarity between proteins is caused by structural and folding constraints.
Compiles structural neighbors of proteins deposited in the Protein Data Bank (PDB). FSN allows to search by a PDB code as a query and provides a list of structurally similar proteins sorted by increasing P-values, as well as links to various statistics about this group of proteins. The database provides a table lists structurally similar proteins with each individual protein in a single row, providing detailed information about each comparison and links to PDB and detailed FATCAT result page.
Provides analysis of protein topology and its modular architecture. ProLego offers an alternative approach to study protein structure topology. It compiles an extensive topology database analyzing different sets of non-redundant representative protein datasets. It can be used for identifying constituent topological modules in proteins of interest, which could be used as “lego-blocks” in protein designing.
Provides access to data from studies on direct coupling analysis (DCA) ability to differentiate between properly folded and misfolded structures. DCA vs. Misfolds is dedicated to studies on DCA, a method that can assist researchers in studying protein structure.
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.
Combines structural coverage leveraged from homology models and experimental protein structures. PMP uses a 3D molecular models in biomedical research to find both experimental structures and theoretical models for a given protein. PMP is an open project for the community offering a unique interface to visualize structural coverage and to analyze the variability of a protein.
Compares predictions of several fold-recognition techniques to the Saccharomyces cerevisiae genome. SPrCY is a database which allows users to search, browse and analyze the generated predictions. It offers an interest with the computational biology community, and the new structural and functional annotations for the yeast genome to help guide new experimental research on this important model organism.