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.
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.
Provides an overview of all missing regions in the Protein Data Bank (PDB) in sequence context. SEQATOMs is derived from PDB and consists of a number of sequence databases and several services, including BLAST and keyword searches, to access the sequence information. It provides four protein sequence databases: (1) PDB SEQATOMS, (2) CATH, (3) PDB SEQRES and (4) DisProt. The BLAST web server allows users to see which regions of the provided query protein correspond with regions without determined structure in PDB.
A comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations. BIGNASim allows direct access to individual trajectory data and pre-computed analyses, as well as global analyses performed on the whole database. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal.
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.
Compiles information about synthetic heterodimeric coiled coils. SYNZIPs is a database cataloguing various interactions connectivities both validated through in vivo and in vitro experiments. The repository provides SYNZIP sequences, structures and interactions coupled to interactions modules and related specifications. The files can be downloaded in various formats including TXT, CSV, XLS or PDB.
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.
Allows users to visualize the ion distributions and provides a summary on quantitative analysis of distributions. IDPM contains several web pages that show different information: (1) the main page, where the distributions of ions are shown in two formats; (2) the introduction page, that supplies the background of the study; (3) the method page, that describes how the datasets are obtained and analyzed; or (4) the amino acid page, that summarizes ion distributions and key observations.
Provides optimized refolding methods/conditions for each protein. REFOLDdb offers users data on about 1900 experimental methods for refolding more than 1600 proteins. It is searchable by sequence similarity; and equipped with statistics that enables the discovery of trends in refolding techniques. The database contains a diverse cross-section of protein architectures, including extracellular domains, subunits, whole proteins and multiple proteins.
A linker database intended for the rational design of linkers for domain fusion. LinkerDB provides linker candidates via user-defined query interface with respect to their Protein Data Bank (PDB) code, sequence, length and secondary structure.
Allows users to store, query, analyze, and share protein design and engineering data. Protabank is an online database that provides a repository for all types of protein engineering (PE) data, spanning a wide range of properties, including those related to activity, binding, stability, folding, and solubility. This database accommodates mutational data obtained from diverse approaches, including computational and other types of rational design, saturation mutagenesis, directed evolution, and deep mutational scanning.
Offers a mix of proteins, most of which come from structural genomics initiatives. CASP8 is composed of three parts: (1) it includes target structure processing, domain parsing, target category defining and prediction quality scoring; (2) it provides sortable tables with assessment scores for all targets and predictions; and (3) it describes each target on a dedicated web page that summarizes its basic features and lists prediction scores for all models.
Provides a set of proteins discovered in proteomics experiments that are present either by accident or through unavoidable contamination of protein samples. cRAP includes the proteins that are employed as molecular weight or mass spectrometry quantitation standards. The proteins available on the platform are divided into five parts: laboratory proteins, dust/contact proteins, molecular weight markers/standard proteins, sigma-aldrich universal protein standard and common viral contaminants.