[ccp4bb]: Announcement: Protein 3D-Pattern Comparison/Search at EMBL

[Rob Russell <russell@embl-heidelberg.de>]

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PINTS (Patterns in Non-homologous Tertiary Structure) is now available
online at http://www.russell.embl.de/pints

It detects similar spatial arrangements of amino acids in protein
structures. There is no requirement for overall fold or sequence
similarity; the method will find all patterns shared between
non-homologous proteins.

PINTS is highly complementary to DALI, VAST, or other methods of whole
structure comparison, for predicting functional details for proteins of
known structure.  PINTS can be used to resolve ambiguities that arise
during fold comparisons (e.g. it can find the one TIM-barrel that matches
a new structure best in terms of function), or suggest convergent
similarities not apparent when comparing sequences or complete structures
(e.g. such as catalytic triads).

PINTS lets one find answers to questions such as:
  Does my new structure contain a known active site / binding site?
  Which residues in my structure form the active site / binding site?
  Can I find an interesting pattern somewhere else in the PDB?
  Which structural patterns are shared between my two proteins?
  And many more...

Matches are evaluated by RMSD (root-mean-square deviation) and a
statistical P-value that assesses the probability of finding the match
just by chance (i.e. without functional implications - similar to the
statistics used in BLAST for sequence searching).

Results are available via WWW or email, and include links for viewing
structural superimpositions via a RasMol interface.

The PINTS server allows you to compare protein structures against one
another or against several databases.

We currently provide the following:

1. Structural patterns of up to ten residues can be compared to
  - 6 non-redundant protein structure databases

2. Whole protein structures of up to 800 residues can be compared to
  - Ligand-binding Sites: residues within 3.0 Å of a HETATM
  - SITE Annotations : residues from all annotated SITEs
  - Surface Residues : residues from PDB_Select 25% exposed
  - Conserved Residues: residues that are more than 80% conserved
        (coming soon)

3. Pair-wise comparisons of two proteins of up to 800 residues each.

Try the server yourself at http://www.russell.embl.de/pints

Alex Stark & Rob Russell

Structural Bioinformatics
EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Tel:+49 6221 387 473/305 (office/lab) FAX:+49 6221 387517
Email: russell@embl.de URL: www.russell.embl.de