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Binding free energy and ligand orientation calculations using a Monte Carlo method with Markov Sate analysis
dc.contributor.author | Lecina-Casas, Daniel |
dc.contributor.author | Takahashi, Ryoji |
dc.contributor.author | Guallar, Victor |
dc.date.accessioned | 2015-06-04T11:06:42Z |
dc.date.available | 2015-06-04T11:06:42Z |
dc.date.issued | 2015-05-05 |
dc.identifier.citation | Lecina-Casas, Daniel; Takahashi, Ryoji; Guallar, Victor. Binding free energy and ligand orientation calculations using a Monte Carlo method with Markov Sate analysis. A: "BSC Doctoral Symposium (2nd: 2015: Barcelona)". 2nd ed. Barcelona: Barcelona Supercomputing Center, 2015, p. 123-124. |
dc.identifier.uri | http://hdl.handle.net/2099/16578 |
dc.description.abstract | Computing binding free energies has great implications in drug design. Using PELE technique, it has been shown that one can get quick and accurate estimations by means of a Markov state model3. We improved our methodology to compute faster binding relative free energy differences, mainly by analysis reducing the sampled region. This possibility opens a way in all-atom drug lead optimization by efficiently scoring a list of potential candidates in terms of binding affinities (approximately in 24hours), while still modeling accurately the protein-drug induced fit. Furthermore, we added information of the ligand orientation allowing us to obtain a better insight of the entrance mechanism. First, we show benchmark results - a series of benzamidine-like inhibitors in trypsin. Then, we apply our method to a more realistic scenario: the binding to a glucocorticoid receptor, and we show the performance for a new benchmark with a larger range of binding free energies (~14 kcal/mol). Simulations are obtained with our new in-house code PELE++, an improvement over the technique presented in references [1,2], (paper in preparation). |
dc.format.extent | 2 p. |
dc.language.iso | eng |
dc.publisher | Barcelona Supercomputing Center |
dc.relation.ispartof | BSC Doctoral Symposium (2nd: 2015: Barcelona) |
dc.rights | Attribution-NonCommercial-NoDerivs 3.0 Spain |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/3.0/es/ |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors |
dc.subject | Àrees temàtiques de la UPC::Enginyeria química::Química orgànica::Bioquímica |
dc.subject.lcsh | High performance computing |
dc.subject.lcsh | Supercomputers |
dc.subject.lcsh | Protein binding |
dc.title | Binding free energy and ligand orientation calculations using a Monte Carlo method with Markov Sate analysis |
dc.type | Conference report |
dc.subject.lemac | Càlcul intensiu (Informàtica) |
dc.subject.lemac | Supercomputadors |
dc.subject.lemac | Fixació de proteïnes |
dc.rights.access | Open Access |
local.citation.author | Lecina-Casas, Daniel; Takahashi, Ryoji; Guallar, Victor |
local.citation.pubplace | Barcelona |
local.citation.publicationName | BSC Doctoral Symposium (2nd: 2015: Barcelona) |
local.citation.startingPage | 123 |
local.citation.endingPage | 124 |
local.citation.edition | 2nd |