Facilitates the exploration of the Protein Data Bank (PDB). PDBeMotif is a search tools allowing users to combining protein sequence, chemical structure and 3D data in a single search. This resource can serve for studying characteristics of the binding sites of single proteins or classes of proteins, such as kinases and the conserved structural features of their immediate environments, either within the same specie or across different species. It can be used online or downloaded and installed locally.
Aims to enable the conformational analysis of intrinsically disordered proteins (IDPs) directly from their experimental chemical shifts (CS). Glutton is a relational database that links existing chemical shift data with corresponding protein 3D structures. User can choose the resolution depending on the specific application. It also includes a script to create structure ensembles based on chemical shifts, or vice-versa.
Contains reference-corrected protein chemical shifts derived from the Biological Magnetic Resonance Bank (BMRB). RefDB was assembled by using the SHIFTX program to predict protein 1H, 13C and 15N chemical shifts from X-ray or NMR (nuclear magnetic resonance) coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts.
A relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research.
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