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New Monte Carlo Based Technique To Study DNA–Ligand Interactions
dc.contributor.author | Cabeza de Vaca, Israel |
dc.contributor.author | Lucas, Fatima |
dc.contributor.author | Guallar, Víctor |
dc.contributor.other | Barcelona Supercomputing Center |
dc.date.accessioned | 2016-03-15T08:28:35Z |
dc.date.available | 2016-11-04T01:30:38Z |
dc.date.issued | 2015-11-03 |
dc.identifier.citation | Cabeza de Vaca, Israel; Lucas, Fatima; Guallar, Víctor. New Monte Carlo Based Technique To Study DNA–Ligand Interactions. "Journal of Chemical Theory and Computation", 03 Novembre 2015, vol. 11, núm. 12, p. 5598-5605. |
dc.identifier.issn | 1549-9618 |
dc.identifier.uri | http://hdl.handle.net/2117/84357 |
dc.description.abstract | We present a new all-atom Monte Carlo technique capable of performing quick and accurate DNA–ligand conformational sampling. In particular, and using the PELE software as a frame, we have introduced an additional force field, an implicit solvent, and an anisotropic network model to effectively map the DNA energy landscape. With these additions, we successfully generated DNA conformations for a test set composed of six DNA fragments of A-DNA and B-DNA. Moreover, trajectories generated for cisplatin and its hydrolysis products identified the best interacting compound and binding site, producing analogous results to microsecond molecular dynamics simulations. Furthermore, a combination of the Monte Carlo trajectories with Markov State Models produced noncovalent binding free energies in good agreement with the published molecular dynamics results, at a significantly lower computational cost. Overall our approach will allow a quick but accurate sampling of DNA–ligand interactions. |
dc.description.sponsorship | The authors thank the Barcelona Supercomputing Center for computational resources. This work was supported by grants from the European Research Council—2009-Adg25027-PELE European project and the Spanish Ministry of Economy and Competitiveness CTQ2013-48287 and “Juan de la Cierva” to F.L. |
dc.format.extent | 8 p. |
dc.language.iso | eng |
dc.publisher | ACS Publications |
dc.subject | Àrees temàtiques de la UPC::Enginyeria mecànica::Impacte ambiental |
dc.subject.lcsh | DNA--Analysis |
dc.subject.other | PELE |
dc.subject.other | DNA |
dc.subject.other | Cisplatin |
dc.subject.other | Markov State Model |
dc.subject.other | Ligand Binding |
dc.title | New Monte Carlo Based Technique To Study DNA–Ligand Interactions |
dc.type | Article |
dc.subject.lemac | ADN |
dc.identifier.doi | 10.1021/acs.jctc.5b00838 |
dc.description.peerreviewed | Peer Reviewed |
dc.relation.publisherversion | http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00838 |
dc.rights.access | Open Access |
dc.description.version | Postprint (author's final draft) |
dc.relation.projectid | info:eu-repo/grantAgreement/EC/FP7/250277/EU/P.E.L.E (Protein Energy Landscape Exploration): a la carte drug design tools/PELE |
dc.relation.projectid | info:eu-repo/grantAgreement/MINECO//CTQ2013-48287-R/ES/DISENYO COMPUTACIONAL RACIONAL DE OXIDOREDUCTASAS PARA APLICACIONES INDUSTRIALES Y TECNOLOGICAS/ |
local.citation.publicationName | Journal of Chemical Theory and Computation |
local.citation.volume | 11 |
local.citation.number | 12 |
local.citation.startingPage | 5598 |
local.citation.endingPage | 5605 |
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