PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS

We present parmbsc1, a new force-field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (~140 μs) covering most of the DNA structural space. Parmbsc1 provides high quality results in diverse systems, solving problems...

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Autores principales: Ivani, Ivan, Dans, Pablo D., Noy, Agnes, Pérez, Alberto, Faustino, Ignacio, Hospital, Adam, Walther, Jürgen, Andrio, Pau, Goñi, Ramon, Balaceanu, Alexandra, Portella, Guillem, Battistini, Federica, Gelpí, Josep Lluis, González, Carlos, Vendruscolo, Michele, Laughton, Charles A., Harris, Sarah A., Case, David A., Orozco, Modesto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2015
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700514/
https://www.ncbi.nlm.nih.gov/pubmed/26569599
http://dx.doi.org/10.1038/nmeth.3658
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author Ivani, Ivan
Dans, Pablo D.
Noy, Agnes
Pérez, Alberto
Faustino, Ignacio
Hospital, Adam
Walther, Jürgen
Andrio, Pau
Goñi, Ramon
Balaceanu, Alexandra
Portella, Guillem
Battistini, Federica
Gelpí, Josep Lluis
González, Carlos
Vendruscolo, Michele
Laughton, Charles A.
Harris, Sarah A.
Case, David A.
Orozco, Modesto
author_facet Ivani, Ivan
Dans, Pablo D.
Noy, Agnes
Pérez, Alberto
Faustino, Ignacio
Hospital, Adam
Walther, Jürgen
Andrio, Pau
Goñi, Ramon
Balaceanu, Alexandra
Portella, Guillem
Battistini, Federica
Gelpí, Josep Lluis
González, Carlos
Vendruscolo, Michele
Laughton, Charles A.
Harris, Sarah A.
Case, David A.
Orozco, Modesto
author_sort Ivani, Ivan
collection PubMed
description We present parmbsc1, a new force-field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (~140 μs) covering most of the DNA structural space. Parmbsc1 provides high quality results in diverse systems, solving problems of previous force-fields. Parmbsc1 aims to be a reference force-field for the study of DNA in the next decade. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
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spelling pubmed-47005142016-05-18 PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS Ivani, Ivan Dans, Pablo D. Noy, Agnes Pérez, Alberto Faustino, Ignacio Hospital, Adam Walther, Jürgen Andrio, Pau Goñi, Ramon Balaceanu, Alexandra Portella, Guillem Battistini, Federica Gelpí, Josep Lluis González, Carlos Vendruscolo, Michele Laughton, Charles A. Harris, Sarah A. Case, David A. Orozco, Modesto Nat Methods Article We present parmbsc1, a new force-field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (~140 μs) covering most of the DNA structural space. Parmbsc1 provides high quality results in diverse systems, solving problems of previous force-fields. Parmbsc1 aims to be a reference force-field for the study of DNA in the next decade. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/. 2015-11-16 2016-01 /pmc/articles/PMC4700514/ /pubmed/26569599 http://dx.doi.org/10.1038/nmeth.3658 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Ivani, Ivan
Dans, Pablo D.
Noy, Agnes
Pérez, Alberto
Faustino, Ignacio
Hospital, Adam
Walther, Jürgen
Andrio, Pau
Goñi, Ramon
Balaceanu, Alexandra
Portella, Guillem
Battistini, Federica
Gelpí, Josep Lluis
González, Carlos
Vendruscolo, Michele
Laughton, Charles A.
Harris, Sarah A.
Case, David A.
Orozco, Modesto
PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title_full PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title_fullStr PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title_full_unstemmed PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title_short PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
title_sort parmbsc1: a refined force-field for dna simulations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700514/
https://www.ncbi.nlm.nih.gov/pubmed/26569599
http://dx.doi.org/10.1038/nmeth.3658
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