Towards a molecular dynamics consensus view of B-DNA flexibility. Export

@article{citeulike:2683039, abstract = {We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.}, author = {P\'{e}rez, Alberto and Lankas, Filip and Luque, F. Javier and Orozco, Modesto}, citeulike-article-id = {2683039}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkn082}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/36/7/2379}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18299282}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18299282}, day = {1}, doi = {10.1093/nar/gkn082}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {dna-entropy, dna-md}, month = {April}, number = {7}, pages = {2379--2394}, posted-at = {2008-12-22 16:50:36}, priority = {2}, title = {Towards a molecular dynamics consensus view of B-DNA flexibility.}, url = {http://dx.doi.org/10.1093/nar/gkn082}, volume = {36}, year = {2008} }

TY - JOUR ID - citeulike:2683039 L3 - citeulike-article-id:2683039 N2 - We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility. IS - 7 JF - Nucleic acids research SN - 1362-4962 EP - 2394 TI - Towards a molecular dynamics consensus view of B-DNA flexibility. VL - 36 SP - 2379 KW - dna-entropy KW - dna-md AU - Pérez, Alberto AU - Lankas, Filip AU - Luque, Javier AU - Orozco, Modesto PY - 2008/04/01/ UR - http://dx.doi.org/10.1093/nar/gkn082 ER -