Adrian Schreyer

CREDO version 11.2009 released!

Structural Interaction Fingerprint (SIFt) for GleevecA 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.

Credo version 4 released

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

Credo Application Programming Interface Tutorial

Fetching objects from the database

# Fetch all structures by UniProt accession
In [1]: structures = StructureAdaptor().fetchAllByUniProt('P53779')
 
In [2]: structures
Out[2]:
[<Structure('1JNK')>,
 <Structure('1PMN')>,
 <Structure('1PMQ')>,
 <Structure('1PMU')>,
 <Structure('1PMV')>,
 <Structure('2B1P')>,
 <Structure('2EXC')>,
 <Structure('2O0U')>,
 <Structure('2O2U')>,
 <Structure('2OK1')>,
 <Structure('2P33')>,
 <Structure('2R9S')>,
 <Structure('2WAJ')>,
 <Structure('2ZDT')>,
 <Structure('2ZDU')>,
 <Structure('3CGF')>,
 <Structure('3CGO')>,

Using The Credo Application Programming Interface with PyMOL

Using The Credo Application Programming Interface with PyMOL

The Credo API provides functions to interact with PyMOL for visualisation purposes, Structural Interaction Fingerprints (SIFts) in particular. This is done by sending commands from the Python interactive shell to PyMOL through an xml-rpc server. Therefore, PyMOL has be be started with the server running:

$ pymol -R

CREDO: A structural interactomics database for drug discovery

The CREDO database has been superseded by a newer version that encompasses the interactions between all residues. A website and RESTful web service to access the database has been developed as well and will be deployed soon.

CREDO paper published in Chemical Biology and Drug Design

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

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