Search results
Results From The WOW.Com Content Network
The data in SMID is derived from the Protein Data Bank (PDB), a database of known protein crystal structures. SMID can be queried by entering a protein GI, domain identifier, PDB ID or SMID ID. The results of a search provide small molecule, protein, and domain information for each interaction identified in the database.
server and repository for protein structure models Protein model databases AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials Protein model databases BioGRID: Samuel Lunenfeld Research Institute: general repository for interaction datasets Protein-protein and other molecular interactions RNA ...
The Protein Data Bank (PDB) is a database of 3D structure data for large biological molecules, such as proteins, DNA, and RNA. PDB is managed by an international organization called the Worldwide Protein Data Bank , which is composed of several local organizations, as. PDBe, PDBj, RCSB, and BMRB.
Examples of protein structures from the PDB (created with UCSF Chimera) Rate of Protein Structure Determination by Method and Year. MX = macromolecular crystallography, 3DEM = 3D Electron Microscopy. [16] The PDB database is updated weekly (UTC+0 Wednesday), along with its holdings list. [17] As of 10 January 2023, the PDB comprised:
The decision was taken to focus on binding data for small molecules with proteins that are drug-targets, or potential drug-targets, and for which the three-dimensional structure is available in the PDB or can potentially be modeled to high accuracy based upon the structure of a similar protein.
The Swiss-model Workspace integrates programs and databases required for protein structure prediction and modelling in a web-based workspace. Depending on the complexity of the modelling task, different modes of use can be applied, in which the user has different levels of control over individual modelling steps: automated mode, alignment mode, and project mode.
First attempt to use sequence and evolutionary features to predict DNA-binding sites in proteins was made by Ahmad et al. (2004) and Ahmad and Sarai (2005). [1] Some methods use structural information to predict DNA-binding sites and therefore require a three-dimensional structure of the protein, while others use only sequence information and ...
The PDBbind database is a comprehensive collection of experimentally measured binding affinity data (Kd, Ki, and IC50) for the protein-ligand complexes deposited in the Protein Data Bank (PDB). [ 1 ] [ 2 ] It thus provides a link between energetic and structural information of protein-ligand complexes, which is of great value to various studies ...