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The ABC (Ascona B-DNA Consortium) initiative was undertaken by an international collaborative effort involving nine research groups. ABC Simulations is a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. Calculations were carried out on the 136 cases embedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of 0.6ms of simulation for systems containing; 24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent 400 gigabytes of data. The DNA trajectory database can be accessed through the following link (http://humphry.chem.wesleyan.edu:8080/MDDNA/). Ten different laboratories all over the world have participated in the ABC2 DNA simulations in which the simulations have been extended up to 50ns with improved protocol.
1. Richard Lavery
Institut de Biologie et Chimie des Protéines
France
http://www.ibcp.fr/fr/ibcp_organigramme.php
Email Id : Richard.Lavery@ibcp.fr
2. Modesto Orozco
Molecular Modeling & Bioinformatics Unit.
Institute for Research in Biomedicine (IRB) & Parc Científic de Barcelona & University of Barcelona
http://mmb.pcb.ub.es/
Email Id : modesto@mmb.pcb.ub.es
3. Roman Osman & Mihaly Mezei
Dept of structural and chemical biology
Mount Sinai School of Medicine, New York
http://atlas.physbio.mssm.edu/index.html
Email Id : Roman.Osman@mssm.edu
4. Charles A. Laughton,
Centre for Bimolecular Sciences,
University of Nottingham, UK
Email Id : charles.laughton@nottingham.ac.uk
5. Jiri Sponer & Nada Spackova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
http://www.ibp.cz/labs/LSDNA/
Email Id : sponer@ncbr.chemi.muni.cz, spackova@ncbr.chemi.muni.cz
6. John Maddocks & Filip Lankas
Swiss Federal Institute of Technology (EPFL)
Lausanne, Switzerland
Email Id : john.maddocks@epfl.ch, filip.lankas@uochb.cas.cz
7. Tom Cheatham
University of Utah
http://www.chpc.utah.edu/~cheatham/
Email Id : tec3@utah.edu
8. Krystyna Zakrzewska
Laboratoire de Biochimie Théorique (URA77 CNRS),
Institut de Biologie Physico-Chimique
Paris
http://www.ibpc.fr/UPR9080/axes_recherches1.html
Email Id : krystyna.zakrzewska@ibcp.fr
9. Surjit B. Dixit and David L. Beveridge
Wesleyan University
http://www.wesleyan.edu/molbiophys/Faculty/Beveridge/beveridge.cv.htm
Email Id : sdixit@zymeworks.com, dbeveridge@wesleyan.edu
10. Thomas C. Bishop
Biology Theoretical Molecular Lab
Center for Computational Science
Tulane University
New Orleans
http://dna.css.tulane.edu
Email Id : bishop@tulane.edu
11. David A. Case
Dept. of Molecular Biology,
The Scripps Research Institute
http://www.scripps.edu/mb/case
Email Id : case@scripps.edu
12. Prof. B. Jayaram,
Supercomputing facility for Bioinformatics and Computational Biology,
Indian Institute of Technology, Delhi, India.
http://www.scfbio-iitd.res.in
Email Id : bjayaram@scfbio-iitd.res.in
