Document Detail


Cell-Dock: high-performance protein-protein docking.
MedLine Citation:
PMID:  22815362     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
SUMMARY: The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized FFT approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200x, while achieving results of similar qualityAvailability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock CONTACT: djimenez@ac.upc.edu; juanf@bsc.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors:
Carles Pons; Daniel Jiménez-González; Cecilia González-Álvarez; Harald Servat; Daniel Cabrera-Benítez; Xavier Aguilar; Juan Fernández-Recio
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-7-19
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  -     Publication Date:  2012 Jul 
Date Detail:
Created Date:  2012-7-20     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Joint BSC-IRB research programme in Computational Biology, Barcelona Supercomputing Center (BSC), Computational Bioinformatics, National Institute of Bioinformatics (INB), Computer Sciences Department, Barcelona Supercomputing Center (BSC), Computer Architecture Department, Universitat Politècnica de Catalunya, Jordi Girona 1, Barcelona 08034, Spain, and PDC Center for High Performance Computing, Stockholm SE-100 44, Sweden.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Network inference using steady-state data and Goldbeter-Koshland kinetics. [corrected].
Next Document:  MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks.