Zobrazeno 1 - 10
of 17
pro vyhledávání: '"Oliver Carrillo"'
Publikováno v:
Nature Communications, Vol 7, Iss 1, Pp 1-14 (2016)
Protein conformational changes are key to a wide range of cellular functions but remain difficult to access experimentally. Here the authors describe eBDIMS, a novel approach to predict intermediates observed in structural transition pathways from ex
Externí odkaz:
https://doaj.org/article/3d956455fb5a419a9e27ee1d23712f42
Autor:
Oliver Carrillo-Parramon, Andrea Amadei, Sara Del Galdo, Vincenzo Barone, Giordano Mancini, Massimiliano Aschi
Publikováno v:
Journal of Chemical Theory and Computation. 13:5506-5514
The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved in several aspects, and implemented in the Gaussian suite of programs for allowing a user-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c3d97d8d7395bdeb725b74417a647c33
https://doi.org/10.1021/acs.jctc.7b00341
https://doi.org/10.1021/acs.jctc.7b00341
Publikováno v:
Journal of Chemical Theory and Computation. 8:2204-2214
We present here the first application of a new algorithm, essential dynamics/molecular dynamics (ED/MD), to the field of small molecule docking. The method uses a previously existing molecular dynamics (MD) ensemble of a protein or protein-drug compl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72e9a0de8c94eb292b0ca0b96c661b13
https://doi.org/10.1021/ct300223c
https://doi.org/10.1021/ct300223c
Autor:
Modesto Orozco, Oliver Carrillo
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 70:892-899
We present here a fast method for the exploration of channels in proteins based on molecular dynamics simulations of probe particles in a discrete grid space defined by an ensemble of protein conformations obtained either experimentally or by out-of-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6cef2531ca15b67bb8c8af191ad7a47e
https://doi.org/10.1002/prot.21592
https://doi.org/10.1002/prot.21592
Publikováno v:
Biophysical Journal. 112:485a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d14250092e232d58f70a6a50dca4c141
https://doi.org/10.1016/j.bpj.2016.11.2625
https://doi.org/10.1016/j.bpj.2016.11.2625
Publikováno v:
Journal of Chemical Theory and Computation
We present a new method for fast molecular dynamics simulations in cases where the new trajectories can be considered a perturbation or a combination of previously stored ones. The method is designed for the postgenomic scenario, where databases such
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e20c0bce1cef2b7659700f6da9f7e612
Autor:
Modesto, Orozco, Laura, Orellana, Adam, Hospital, Athi N, Naganathan, Agustí, Emperador, Oliver, Carrillo, J L, Gelpí
Publikováno v:
Advances in protein chemistry and structural biology. 85
Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::652f99e82c35a5897e490fcfa565fcfb
https://pubmed.ncbi.nlm.nih.gov/21920324
https://pubmed.ncbi.nlm.nih.gov/21920324
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories
Autor:
Tim Meyer, Marco D'Abramo, Adam Hospital, Manuel Rueda, Carles Ferrer-Costa, Alberto Pérez, Oliver Carrillo, Jordi Camps, Carles Fenollosa, Dmitry Repchevsky, Josep Lluis Gelpí, Modesto Orozco
Publikováno v:
Structure
SummaryMore than 1700 trajectories of proteins representative of monomeric soluble structures in the protein data bank (PDB) have been obtained by means of state-of-the-art atomistic molecular dynamics simulations in near-physiological conditions. Th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a117d2b288181113afe7c808b5b5dd24
https://pubmed.ncbi.nlm.nih.gov/21070939
https://pubmed.ncbi.nlm.nih.gov/21070939
Autor:
Alessandro Feis, Giulietta Smulevich, Francesca Spyrakis, F. Javier Luque, Peter Schmidtke, Paola Dominici, Elena Grandi, Andrea Mozzarelli, Silvia Brogioni, Stefano Bruno, Serena Faggiano, Stefania Abbruzzetti, Oliver Carrillo, Axel Bidon-Chanal, Cristiano Viappiani, Alessandra Astegno, Pietro Cozzini
Publikováno v:
The journal of physical chemistry. B. 113(49)
The increasing number of nonsymbiotic plant hemoglobins discovered in genomic studies in the past decade raises intriguing questions about their physiological role. Among them, the nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana deserves parti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::588e24310250c5eb07dec13fd25ea970
https://pubmed.ncbi.nlm.nih.gov/19954242
https://pubmed.ncbi.nlm.nih.gov/19954242
Autor:
Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda, Carles Ferrer, Antonio Valencia, Alberto Pérez, Oliver Carrillo, Juan Fernandez-Recio, Xavier de la Cruz, F. Javier Luque
Publikováno v:
Computational Studies of RNA and DNA ISBN: 9781402047947
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e4e33ac89fdc499a491ee11d05ab65eb
https://doi.org/10.1007/978-1-4020-4851-3_5
https://doi.org/10.1007/978-1-4020-4851-3_5
