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 Email Id : Richard.Lavery@ibcp.fr 2. Modesto Orozco Email Id : modesto@mmb.pcb.ub.es 3. Roman Osman & Mihaly Mezei Email Id : Roman.Osman@mssm.edu 4. Charles A. Laughton, Email Id : charles.laughton@nottingham.ac.uk 5. Jiri Sponer & Nada Spackova Email Id : sponer@ncbr.chemi.muni.cz, spackova@ncbr.chemi.muni.cz 6. John Maddocks & Filip Lankas Email Id : john.maddocks@epfl.ch, filip.lankas@uochb.cas.cz
Email Id : tec3@utah.edu 8. Krystyna Zakrzewska Email Id : krystyna.zakrzewska@ibcp.fr 9. Surjit B. Dixit and David L. Beveridge Email Id : sdixit@zymeworks.com, dbeveridge@wesleyan.edu
Email Id : bishop@tulane.edu 11. David A. Case Email Id : case@scripps.edu 12. Prof. B. Jayaram, Email Id : bjayaram@scfbio-iitd.res.in
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References |
[1] Marco Passi, John H.Maddocks, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham III, Pablo D. Dans, B. Jayaram, Filip Lankas, Charles Laughton, Jonathan Mitchell, Roman Osman, Modesto Orozco, Alberto Perez, DaivaPetkeciuvite, Nada Spackova, Jiri Sponer, KrystynaZakrzewska, Richard Lavery, "{mu}ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA"., Nucl. Acids Res., 2014.doi: 10.1093/nar/gku855 . http://nar.oxfordjournals.org/content/early/2014/09/26/nar.gku855.ful |
[2] A systematic molecular dynamics study of nearestneighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Read Paper |
[3] Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps. Read Paper |