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10.1371/journal.pcbi.1004631 http://scihub22266oqcxt.onion/10.1371/journal.pcbi.1004631 C4689557!4689557!26657165     free     free     free Deprecated: Implicit conversion from float 219.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 219.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 219.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 219.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       PLoS+Comput+Biol 2015 ; 11 (12): ä Nephropedia Template TP {{tp|p=26657165|t=2015. Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics |pdf=|usr=}}{{26657165}} gab.com Text Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics JO: PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=26657165 #FOAvip The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ? BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0??OLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition. Twit Text FOAVip Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics ????PLoS Comput Biol http://www.kidney.de/pget.php?&tw=1&pmid=26657165 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=26657165 #FOAvip English Wikipedia <ref>{{Cite pmid|26657165}}</ref> Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics #MMPMID26657165 Ben Imeddourene A; Elbahnsi A; Guéroult M; Oguey C; Foloppe N; Hartmann B PLoS Comput Biol 2015[Dec]; 11 (12): ä PMID26657165show ga The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ? BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0??OLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition. äSimulations Meet Experiment to Reveal New Insights into DNA Intrinsic (epmc).pdf DeepDyve Pubget Overpricing