A new version of the CREDO database has been released including 40,091 PDB structures. New features include:

• Ring interaction geometries have been implemented according to Chakrabarti, P. & Bhattacharyya, R. Geometry of nonbonded interactions involving planar groups in proteins. Progress in Biophysics and Molecular Biology 95, 83-137 (2007).
• New RECAP rules have been introduced to better fragment biomolecules, e.g. breaking of phosphate bonds and cleavage of sulphates.
• New flags for residues have been introduced to label mutated and modified amino acids (through sequence-to-structure mapping)
• SCOP version 1.75
• Structural interaction fingerprints are now available on a UniProt residue level and SIFt clusters part of the public version.
• Donor-Pi, Cation-Pi as well as Carbon-Pi atom-ring interactions are now available in dedicated tables (from which the Contacts table can be updated).
• SCOP- and UniProt-based SIFt clustering

For instructions on how to download and install the CREDO database, please go to the CREDO website.

Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database.

Chem Biol Drug Des. 2009 Nov;74(5):457-67

Authors: Higueruelo AP, Schreyer A, Bickerton GR, Pitt WR, Groom CR, Blundell TL

A paper in Angewandte Chemie International Edition on the results of a fragment-based TB drug discovery project, done in collaboration with Professor Chris Abell's group in the Department of Chemistry, is now available. CLICK HERE TO ACCESS

Our review entitled "Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics" in Molecular Biosystems can now be accessed online prior to full publication.
CLICK HERE TO ACCESS

A new version of the Credo database has been released with the following changes:

• The data generation scripts are now based on OEChem 1.7.0
• Residues found in contact with a ligand are now compared against the polymer sequence defined in the mmCIF form to eliminate possible ligand-ligand contacts in structures where the ligand syntax is poorly defined
• Some column data type were changed to avoid truncation of large text fields

This is the crystal structure by Dr Luca Pellegrini of a complex between human recombinase Rad51 with the fourth BRC repeat from breast cancer associated protein BRCA2. We are applying fragment based drug discovery methods to target this protein-protein interaction with aim to develop small molecule inhibtors that can be used both as chemical tools for research and as lead compounds for eventual drug development.

PDB:

1n0w

Reference

CREDO: A Protein–Ligand Interaction Database for Drug Discovery

Harnessing data from the growing number of protein–ligand complexes in the Protein Data Bank is an important task in drug discovery. In order to benefit from the abundance of three-dimensional structures, structural data must be integrated with sequence as well as chemical data and the protein–small molecule interactions characterized structurally at the inter-atomic level. In this study, we present CREDO, a new publicly available database of protein–ligand interactions, which represents contacts as structural interaction fingerprints, implements novel features and is completely scriptable through its application programming interface. Features of CREDO include implementation of molecular shape descriptors with ultrafast shape recognition, fragmentation of ligands in the Protein Data Bank, sequence-to-structure mapping and the identification of approved drugs. Selected analyses of these key features are presented to highlight a range of potential applications of CREDO. The CREDO dataset has been released into the public domain together with the application programming interface under a Creative Commons license at http://www-cryst.bioc.cam.ac.uk/credo. We believe that the free availability and numerous features of CREDO database will be useful not only for commercial but also for academia-driven drug discovery programmes.

http://www3.interscience.wiley.com/journal/121654603/abstract