PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
نویسندگان
چکیده
منابع مشابه
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determ...
متن کاملPLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
MOTIVATION A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions t...
متن کاملAffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB
AffinDB is a database of affinity data for structurally resolved protein-ligand complexes from the Protein Data Bank (PDB). It is freely accessible at http://www.agklebe.de/affinity. Affinity data are collected from the scientific literature, both from primary sources describing the original experimental work of affinity determination and from secondary references which report affinity values d...
متن کاملPDBToSDF: Create ligand structure files from PDB file
Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bo...
متن کاملAnalytical Processing of PDB Ligand Fragments and Protein Environment directly on the Web
The PDB protein-ligand complexes are the main public resource that provides detailed chemical environment information for atomic level interactions between the ligand and the protein. In order to investigate relevant research questions PDB users have often to extract this data manually or semiautomatically. The public MSD search relational database hosted by the EBI has been designed to address...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2004
ISSN: 1362-4962
DOI: 10.1093/nar/gki059