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Databases

by morris last modified 2009-05-29 11:13

Here are some databases useful for finding structures for docking and virtual screening.

Macromolecules and Small Molecule Complexes:

PDB
the Protein Data Bank from the Research Collaboratory for Structural Bioinformatics.
BindingDB
from Michael Gilson's Laboratory, provides a rich repository of structural and thermocalorimetric data about ligand-protein interactions, including standard free energy, enthalpy and entropy changes upon binding, ΔG°, ΔH°, and -TΔS° for a small but growing number of complexes.
  1. Liu, T.; Lin, Y.; Wen, X.; Jorissen, R. N.; Gilson, M. K. (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res, 35: D198-201.
  2. Chen, X.; Lin, Y.; Liu, M.; Gilson, M. K. (2002) The Binding Database: data management and interface design. Bioinformatics, 18: 130-139.
  3. Chen, X.; Lin, Y.; Gilson, M. K. (2001) The binding database: overview and user's guide. Biopolymers, 61: 127-141.
  4. Chen, X.; Liu, M.; Gilson, M. K. (2001) BindingDB: a web-accessible molecular recognition database. Comb Chem High Throughput Screen, 4: 719-725.
BindingMOAD - Mother Of All Databases
from Heather Carlson's Laboratory, it is "a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding... [its] goal is to be the largest collection of well resolved (2.5 Å or better) protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature... Ligands may be a peptide of 10 amino acids or less; oligonucleotide of 4 nucleotides or less; small organic molecule (e.g. ibuprofen); cofactor (e.g. NADPH). Ligands are not: crystallographic additives (e.g. polythylene glycol); salts (Cl-, phosphates); buffers (e.g. Tris, CHAPS); metals (e.g. Rb+, Zn2+); metallic catalytic centers (e.g. FeS, NiFe); or solvents (e.g. DMSO). The binding data are extracted from the literature, by searching through the primary reference of each PDB entry looking for Kd, Ki, and IC50 data.
  1. Hu, L.; Benson, M.L.; Smith, R.D.; Lerner, M.G.; Carlson, H.A. (2005). Binding MOAD (Mother Of All Databases). Proteins, 60: 333-40.
PDBbind
The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). It was officially launched in May 2004, and is hosted at the University of Michigan, USA; an additional server in Shanghai, China, PDBbind-CN, is also available.
  1. Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. (2005) "The PDBbind Database: Methodologies and updates", J. Med. Chem., 48: 4111-4119.
  2. Wang, R.; Fang, X.; Lu, Y.; Wang, S. (2004) "The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures", J. Med. Chem., 47, 2977-2980.

Small Molecules:

NCI Diversity Set II
is a set of just about 2000 compounds representing the broader chemical space of the 140,000 or so compounds in its holdings. There are 2D and 3D structures available, plus the Olson Laboratory distributes the NCI Diversity Set formatted for use in AutoDock [630KB].
ZINC
ZINC Is Not Commercial (a recursive acronym just like GNU is Not Unix) - a tremendous and free source of more than 4 million commercially-available small molecule structures for virtual screening (ZINC is not commercial, but most of the compounds in its database are for sale...).
  1. Irwin, J. J.; Shoichet, B. K. (2005) ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model, 45: 177-182.
PubChem
"PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative." There is a Structure Search option, that can retrieve the IUPAC name, molecular weight, biological data, and even links to structural data.

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