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Alex Rodriguez
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Clustering by fast search and find of density peaks
A Rodriguez, A Laio
science 344 (6191), 1492-1496, 2014
41272014
Estimating the intrinsic dimension of datasets by a minimal neighborhood information
E Facco, M d’Errico, A Rodriguez, A Laio
Scientific reports 7 (1), 12140, 2017
1862017
Unsupervised learning methods for molecular simulation data
A Glielmo, BE Husic, A Rodriguez, C Clementi, F Noé, A Laio
Chemical Reviews 121 (16), 9722-9758, 2021
992021
Computing the free energy without collective variables
A Rodriguez, M d’Errico, E Facco, A Laio
Journal of chemical theory and computation 14 (3), 1206-1215, 2018
472018
Automatic topography of high-dimensional data sets by non-parametric density peak clustering
M d’Errico, E Facco, A Laio, A Rodriguez
Information Sciences 560, 476-492, 2021
442021
METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
T Giorgino, A Laio, A Rodriguez
Computer Physics Communications 217, 204-209, 2017
372017
Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate
A Rodríguez, C Oliva, M Gonzalez, M van der Kamp, AJ Mulholland
The Journal of Physical Chemistry B 111 (44), 12909-12915, 2007
372007
A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels
LMR Napolitano, I Bisha, M De March, A Marchesi, M Arcangeletti, ...
Proceedings of the National Academy of Sciences 112 (27), E3619-E3628, 2015
302015
Unsupervised learning universal critical behavior via the intrinsic dimension
T Mendes-Santos, X Turkeshi, M Dalmonte, A Rodriguez
Physical Review X 11 (1), 011040, 2021
272021
Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
I Bisha, A Rodriguez, A Laio, A Magistrato
PLoS computational biology 10 (12), e1004017, 2014
232014
Synthesis and evaluation of diverse analogs of amygdalin as potential peptidomimetics of peptide T
E Araya, A Rodriguez, J Rubio, A Spada, J Joglar, A Llebaria, C Lagunas, ...
Bioorganic & medicinal chemistry letters 15 (5), 1493-1496, 2005
232005
Conformational Diversity in Contryphans from Conus Venom: cistrans Isomerisation and Aromatic/Proline Interactions in the 23‐Membered Ring of a 7‐Residue …
R Sonti, KH Gowd, KNS Rao, S Ragothama, A Rodriguez, JJ Perez, ...
Chemistry–A European Journal 19 (45), 15175-15189, 2013
222013
Candidate binding sites for allosteric inhibition of the SARS-CoV-2 main protease from the analysis of large-scale molecular dynamics simulations
M Carli, G Sormani, A Rodriguez, A Laio
The journal of physical chemistry letters 12 (1), 65-72, 2020
202020
The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models
G Pinamonti, F Paul, F Noé, A Rodriguez, G Bussi
The Journal of chemical physics 150 (15), 154123, 2019
202019
Designing high-affinity peptides for organic molecules by explicit solvent molecular dynamics
I Gladich, A Rodriguez, RP Hong Enriquez, F Guida, F Berti, A Laio
The Journal of Physical Chemistry B 119 (41), 12963-12969, 2015
192015
An efficient algorithm to perform local concerted movements of a chain molecule
S Zamuner, A Rodriguez, F Seno, A Trovato
PloS one 10 (3), e0118342, 2015
192015
Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent
A Rodriguez, P Mokoema, F Corcho, K Bisetty, JJ Perez
The Journal of Physical Chemistry B 115 (6), 1440-1449, 2011
192011
Computational design of cyclic peptides for the customized oriented immobilization of globular proteins
MA Soler, A Rodriguez, A Russo, AF Adedeji, CJD Foumthuim, ...
Physical Chemistry Chemical Physics 19 (4), 2740-2748, 2017
182017
A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B
A Rodríguez, C Oliva, M González
Physical Chemistry Chemical Physics 12 (28), 8001-8015, 2010
172010
Intrinsic dimension of path integrals: Data-mining quantum criticality and emergent simplicity
T Mendes-Santos, A Angelone, A Rodriguez, R Fazio, M Dalmonte
PRX Quantum 2 (3), 030332, 2021
142021
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