Data Challenge WISDOM

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AUTODOCK

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. It is free for academic.

Main applications:

Binding mode prediction of ligands in a protein environment It includes 2 methods : a Monte Carlo simulated annealing and a Lamarcian genetic algorithm
Automated high-throughput screening

References:

Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J. (1998), J. Computational Chemistry, 19: 1639-1662. "Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function".

w3.to/autodock

FLEXX

FlexX is an extremely fast, robust, and highly configurable (FlexX-able) computer program for predicting protein-ligand interactions. It is a licensed software.SCAI gives access to FlexX within the framework of this collaboration for a limited time.

Main applications:

Binding mode prediction For a protein with known three-dimensional structure and a small ligand molecule, FlexX predicts the geometry of the protein-ligand complex and estimates the binding affinity in less than 15 seconds.
Virtual high-throughput screening (vHTS) With FlexX you can screen a database consisting of ~100.000 compounds in about 8 hours on a 30-node cluster - fully automated

References:

M. Rarey, B. Kramer, T. Lengauer & G. Klebe
Predicting Receptor-Ligand interactions by an incremental construction algorithm, J. Mol. Biol. 261: 470-489, 1996

www.biosolveit.de/FlexX

FlexX license server usage on the EGEE infrastructure

The usage of the first commercial docking software with floating licenses on the EGEE infrastructure is a good success. There were total of 3000 floating licenses given by BioSolveIT to SCAI, fraunhofer, Germany and these licenses were distributed on the grid. Maximum number of used licenses was 1008 on a particular day during the Data Challenge, which is proportional to the running jobs.
Accessing floating licenses on the GRID (which involved firewalls) needs opened ports on the remote side institutes in the VO-BIOMED. Only few institutes had not these ports opened for security reasons.
During the FlexX data challenge, the server failed few times. The reason is the number limitation of file descriptors on the system and the problem was solved. Apart from this failure, there was continuous usage of floating licenses during the FlexX Data Challenge period. The server has not any direct connection to LCG middleware. In the future, it would be nice to integrate the server into the grid, so that we can check certificates of the biomed organization in order to grant licenses.
Finally the Commercial FlexX docking software with floating licenses was a success.

ZINC

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 3.3 million compounds in ready-to-dock. Compounds in ZINC may be ordered directly from the vendors.

References:

Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82

blaster.docking.org/zinc

CHEMBRIDGE

ChemBridge Corporation is a leading global discovery chemistry contract research organization (CRO) and premier provider of screening libraries for small molecule drug discovery. Best hits found by the Data Challenge will be analyzed on the screening experimental platform.

chembridge.com/chembridge

PDB

PDB is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. Malaria target structures from PDB were improved by SCAI for the Data Challenge

References:

H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne
The Protein Data Bank
Nucleic Acids Research, 28 pp. 235-242 (2000)