University of Cambridge, Department of Biochemistry

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CREDO

JNK inhibitors grid mode example (2P33, 3FV8)

Tue, 27/10/2009 - 16:04 — Adrian
JNK inhibitors grid mode example (2P33, 3FV8)

In [1]: from credopymol import *
 
# Fetch Both Structures from the database and load into PyMOL
In [2]: s1 = StructureAdaptor().fetchByPDB('2P33')
In [3]: s1.load()
In [4]: s2 = StructureAdaptor().fetchByPDB('3fv8')
In [5]: s2.load()
 
# Align both chains with the PyMOL super command
In [6]: s1.Chains[0].align(s2.Chains[0]) 
 
# Show contacts
In [7]: l1 = s1.Ligands[0]
In [8]: l1.showContacts()
In [9]: l2 = s2.Ligands[0]
In [10]: l2.showContacts()
 
# Change to grid mode
In [11]: pymol.set('grid_mode',1)

CREDO version 11.2009 released!

Tue, 27/10/2009 - 12:18 — Adrian

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.

Comparison of fragment structural interactions in PyMOL grid mode

Mon, 26/10/2009 - 14:28 — Adrian
Comparison of fragment structural interactions in PyMOL grid mode

the screenshot shows an example of how structures (chains) can be aligned including the interactions of their ligands with the help of the credoscript PyMOL interface. The structures are 2C5O and 2VTA respectively. The structures are represented in grid mode to view and rotate them both in parallel.

Halogen bonds

Mon, 26/10/2009 - 14:05 — Adrian
Halogen bonds

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')>,

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.

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