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BSDB / Biomolecule Stretching 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.
SEQATOMs
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.
BIGNASim
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.
IDPM / Ion Distribution in Protein Molecules
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.
ProtaBank
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.
cRAP / common Repository of Adventitious Proteins
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.
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