The BioPAUÁ Project: A Portal for Molecular Dynamics Using Grid Environment

This paper describes BioPAUA Project, a new portal for Molecular Dynamics (MD) simulations over a computational grid environment. It integrates MD simulations and analyses tools with grid technologies to provide support to biomolecular in silico experiments. The objective of BioPAUA Project is to offer a tool, as well the facility, for researches working in several important fields (e.g., bioinformatics, structural biology, biochemistry, medicinal chemistry, biopharmacology). At first, the possible user does not need any special skill in MD simulations, however, advanced ones are also well contemplated. The project methodology is based on MYGRID middleware and uses GROMACS package in order to run simulations. This work is developed by LNCC/MCT, with IBCCF/UFRJ collaboration, and supported by HP Brazil R&D.

[1]  P. Kollman,et al.  Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. D. Figueroa-Villar,et al.  Molecular dynamics of the interaction of Plasmodium falciparum and human serine hydroxymethyltransferase with 5-formyl-6-hydrofolic acid analogues: design of new potential antimalarials , 2006 .

[3]  A Rojnuckarin,et al.  Bimolecular reaction simulation using Weighted Ensemble Brownian dynamics and the University of Houston Brownian Dynamics program. , 2000, Biophysical journal.

[4]  Francisco Brasileiro,et al.  Scheduling in Bag-of-Task grids: the PAUA case , 2004 .

[5]  J. Kahn,et al.  HIV-1 protease inhibitors. A review for clinicians. , 1997 .

[6]  Keith Marzullo,et al.  Open Grid: A User-Centric Approach for Grid Computing , 2001 .

[7]  K. Chou,et al.  Predicting human immunodeficiency virus protease cleavage sites in proteins by a discriminant function method , 1996, Proteins.

[8]  Jack R. Collins,et al.  Flap opening in HIV-1 protease simulated by ‘activated’ molecular dynamics , 1995, Nature Structural Biology.

[9]  Ian T. Foster,et al.  The Anatomy of the Grid: Enabling Scalable Virtual Organizations , 2001, Int. J. High Perform. Comput. Appl..

[10]  Chu-Sing Yang,et al.  2003 International Conference on Parallel Processing , 2003 .

[11]  Isaac D. Scherson,et al.  Efficient Parallel Job Scheduling Using Gang Service , 2001, Int. J. Found. Comput. Sci..

[12]  Scott Klasky,et al.  Grids for experimental science: the virtual control room , 2004, Proceedings of the Second International Workshop on Challenges of Large Applications in Distributed Environments, 2004. CLADE 2004..

[13]  D. M. F. Aalten,et al.  PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules , 1996, J. Comput. Aided Mol. Des..

[14]  P. Pascutti,et al.  Molecular dynamics simulations applied to the study of subtypes of HIV-1 protease common to Brazil, Africa, and Asia , 2007, Cell Biochemistry and Biophysics.

[15]  P. Volberding,et al.  HIV-1 protease inhibitors , 1992 .

[16]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[17]  K. Hertogs,et al.  Genotypic and Phenotypic Evidence of Different Drug-Resistance Mutation Patterns between B and Non-B Subtype Isolates of Human Immunodeficiency Virus Type 1 found in Brazilian Patients Failing HAART , 2004, Virus Genes.

[18]  C. Schiffer,et al.  How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. , 2000, Journal of molecular biology.

[19]  Nazareno Andrade,et al.  Discouraging free riding in a peer-to-peer CPU-sharing grid , 2004, Proceedings. 13th IEEE International Symposium on High performance Distributed Computing, 2004..

[20]  Ian T. Foster,et al.  Data management and transfer in high-performance computational grid environments , 2002, Parallel Comput..

[21]  Nazareno Andrade,et al.  Peer-to-peer grid computing with the OurGrid Community , 2005 .