HADDOCK in a CONDOR environment

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HADDOCK a great application to run in a condor
environment
HADDOCK in a CONDOR environment
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HADDOCK (High Ambiguity Driven biomolecular
DOCKing) is an approach to the structure
determination of protein-protein and protein-DNA
complexes that makes use of biochemical and/or
biophysical interaction data. Cyril Dominguez,
Rolf Boelens and Alexandre M.J.J. Bonvin
(2003). HADDOCK a protein-protein docking
approach based on biochemical and/or biophysical
information. J. Am. Chem. Soc. 125, 1731-1737.
What is HADDOCK ?
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In the field of molecular modeling, docking is a
method which predicts the preferred orientation
of one molecule to a second when bound to each
other to form a stable complex.
What is DOCKING ?
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Proteins Why is all of this important ?
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RNA polymerase RNA Ribosome ...
DNA Why is all of this important ?
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HADDOCK consists of a collection of python and
csh scripts that setup, analyze and score CNS
inputs and outputs in order to make CNS produce
the best complex structures. CNSsolve has been
designed to provide a flexible multi-level
hierachical approach for the most commonly used
algorithms in macromolecular structure
determination.
analyze, score, select setup
analyze, score, (select) setup
analyze score
How HADDOCK works
setup
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Randomization rigid body docking 1000
5min CNS Jobs
Semi fully flexible simulated annealing 200
20min CNS Jobs
Final refinement with explicit solvent 200
40min CNS Jobs
How HADDOCK works in a condor enviroment
Times where taken in a AMD athlonXP 2800
(Thoroughbred)
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An Example LexA protein-DNA docking
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HB tyr 44.a oh cyt 113.b 02 VW lys 51.a cyt
11 gua 110 ile 48.a ade 10.b thy 112.b ade
9.b met 52.a 6A asp 43.a 5A ade 10.b
5A ade 9.b lys 47.a 6A
HB tyr 44.a oh thy 114.b lys 47.a nz ade 9.b
nb ade 10.b o4' tyr 44.a o VW met 52.a 6A ile
48.a cyt 11.b ade 10.b lys 51.a 5a
HB tyr 44.a oh gua 8b n2 lys 51.a nz cyt 11.b
o2 VW ile 48.a tyr 112.b ade 10.b met 52.a
5A cyt 11.b lys 47.a 5A cyt 113.b thy 114.b
An Example LexA protien-DNA docking
HB gln 50.a ne2cyt 113 VW lys 51.a cyt 11.b met
52.a cyt 11.b ile 48.a 5A cyt 11.b lys 47.a ade
9.b tyr 44.a 6A
HB tyr 44.a oh thy 114.b o4' lys 51.a nz thy
111.b o2 thy 112.b o4' VW met 52.a cyt 11.b Ile
48.a ade 10.b cyt 113.b lys 47.a thy 114.b
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UAB Departament de Genètica i Microbiologia Jordi
Barbé Susana Campoy
Universiteit Utrecht NMR Group Alexandre Bonvin
Acknowledgements
UAB Computer Architecture Operating Systems
Department Miquel Àngel Senar