@article{4175b9b02b0148739b4cdf5dc22f6808,
title = "Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps",
abstract = "We describe herein 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. This initiative was undertaken by an international collaborative effort involving nine research groups, the {"}Ascona B-DNA Consortium{"} (ABC). Calculations were carried out on the 136 cases imbedded 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 ∼-0.6 μs of simulation for systems containing ∞24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent ∞400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.",
author = "Beveridge, {David L.} and Gabriela Barreiro and Byun, {K. Suzie} and Case, {David A.} and Cheatham, {Thomas E.} and Dixit, {Surjit B.} and Emmanuel Giudice and Filip Lankas and Richard Lavery and Maddocks, {John H.} and Roman Osman and Eleanore Seibert and Heinz Sklenar and Gautier Stoll and Thayer, {Kelly M.} and P{\'e}ter Varnai and Young, {Matthew A.}",
note = "Funding Information: The ABC collaboration commenced at a workshop on “Atomistic to Continuum Models for Long Molecules and Thin Films” held at the Mte Verita Conference Centre in Ascona, Switzerland in July, 2001. Funding for this meeting was provided by the Center Stefano Franscini, the European Office of Aerospace Research and Development, Air Force Office of Scientific Research, United States Air Force Research Laboratory, United States Office of Naval Research (Europe), Compaq, the European Science Foundation-Programme SIMU, and the Ecole Polytechnique Federale de Lausanne (EPLF), Switzerland. The ABC project was advanced in a Centre Europ{\'e}en de Calcul Atomique et Mol{\'e}culaire (CECAM) workshop in Lyon, France the next year, and a meeting, “DNA and Beyond: Structure, Dynamics and Interactions,” held at the EPFL in April, 2003, sponsored by the Bernoulli Center of the EPFL and Hewlett-Packard, Inc. Funding Information: Generous support for both these meetings is gratefully acknowledged. Prof. Beveridge acknowledges support for this research from the National Institute of General Medical Sciences (NIGMS) (grant no. GM37909) and the Keck Center for Integrative Genomics at Wesleyan University. The participation of Kelly M. Thayer in this project was supported by an NIGMS training grant in Molecular Biophysics to Wesleyan University (grant no. GM 08271). Dr. Gabriela Barreiro acknowledges CNPq/Brazil (Conselho Nacional de Desenvolvimento Cient{\'i}fico e Tecnol{\'o}gico) for a postdoctoral fellowship. Supercomputer time was generously provided under the auspices of the Partnerships for Advanced Computational Infrastructure program on the facilities of the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Champaign/Urbana. The contribution of Dr. Richard Lavery and co-workers was supported by grants from the Centre National de la Recherche Scientifique, France. Dr. Peter Varnai thanks the Wellcome Trust for an International Prize Travelling Research Postdoctoral Fellowship (grant reference 060078). Prof. Cheathem acknowledges computational time from a National Research Advisory Council allocation (MCA01S027) and friendly user time on computer hardware at the University of Kentucky, the Pittsburgh Supercomputing Center, and the NCSA. Prof Osman acknowledges support from National Cancer Institute grant CA 63317. Eleanore Seibert was supported by National Institutes of Health training grants GM08553 and CA78207. Prof. Cheatham also acknowledges support from the Center for High Performance Computing at the University of Utah and financial support from the National Science Foundation (CHE-0326027). Dr. Filip Lankas acknowledges the support provided by the Centre for Complex Molecular Systems and Biomolecules (LN00A032) financed by the Ministry of Education of the Czech Republic. Prof Maddocks acknowledges the support for this research provided by the Swiss National Science Foundation and via a research collaboration between the EPFL and Hewlett-Packard.",
year = "2004",
month = dec,
doi = "10.1529/biophysj.104.045252",
language = "English",
volume = "87",
pages = "3799--3813",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Cell Press",
number = "6",
}