Walter Rocchia
Walter Rocchia
Senior Researcher at Italian Institute of Technology
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Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
W Rocchia, E Alexov, B Honig
The Journal of Physical Chemistry B 105 (28), 6507-6514, 2001
Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and …
W Rocchia, S Sridharan, A Nicholls, E Alexov, A Chiabrera, B Honig
Journal of computational chemistry 23 (1), 128-137, 2002
Wearable, redundant fabric-based sensor arrays for reconstruction of body segment posture
F Lorussi, W Rocchia, EP Scilingo, A Tognetti, D De Rossi
IEEE Sensors Journal 4 (6), 807-818, 2004
A catalytically silent FAAH-1 variant drives anandamide transport in neurons
J Fu, G Bottegoni, O Sasso, R Bertorelli, W Rocchia, M Masetti, A Guijarro, ...
Nature neuroscience 15 (1), 64-69, 2012
Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5
JS Patel, A Berteotti, S Ronsisvalle, W Rocchia, A Cavalli
Journal of chemical information and modeling 54 (2), 470-480, 2014
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
L Mollica, S Decherchi, SR Zia, R Gaspari, A Cavalli, W Rocchia
Scientific reports 5 (1), 1-12, 2015
The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning
S Decherchi, A Berteotti, G Bottegoni, W Rocchia, A Cavalli
Nature communications 6 (1), 1-10, 2015
Systematic exploitation of multiple receptor conformations for virtual ligand screening
G Bottegoni, W Rocchia, M Rueda, R Abagyan, A Cavalli
PLoS One 6 (5), e18845, 2011
A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale
S Decherchi, W Rocchia
PloS one 8 (4), e59744, 2013
Mapping all-atom models onto one-bead coarse-grained models: General properties and applications to a minimal polypeptide model
V Tozzini, W Rocchia, JA McCammon
Journal of chemical theory and computation 2 (3), 667-673, 2006
Green fluorescent protein ground states: the influence of a second protonation site near the chromophore
R Bizzarri, R Nifosì, S Abbruzzetti, W Rocchia, S Guidi, D Arosio, G Garau, ...
Biochemistry 46 (18), 5494-5504, 2007
Kinetic and structural insights into the mechanism of binding of sulfonamides to human carbonic anhydrase by computational and experimental studies
R Gaspari, C Rechlin, A Heine, G Bottegoni, W Rocchia, D Schwarz, ...
Journal of medicinal chemistry 59 (9), 4245-4256, 2016
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets
G Bottegoni, W Rocchia, M Recanatini, A Cavalli
Bioinformatics 22 (14), e58-e65, 2006
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure
G Neshich, W Rocchia, AL Mancini, MEB Yamagishi, PR Kuser, R Fileto, ...
Nucleic acids research 32 (suppl_2), W595-W601, 2004
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
F Spyrakis, P Benedetti, S Decherchi, W Rocchia, A Cavalli, S Alcaro, ...
Journal of chemical information and modeling 55 (10), 2256-2274, 2015
Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution
S Decherchi, J Colmenares, CE Catalano, M Spagnuolo, E Alexov, ...
Communications in computational physics 13 (1), 61-89, 2013
DelPhi web server: a comprehensive online suite for electostatic calculations of biological macromolecules and their complexes
S Sarkar, S Witham, J Zhang, M Zhenirovskyy, W Rocchia, E Alexov
Commun. Comput. Phys. 13 (1), 269-284, 2012
Kinetics of drug binding and residence time
M Bernetti, M Masetti, W Rocchia, A Cavalli
Annual review of physical chemistry 70, 143-171, 2019
dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking
D Spiliotopoulos, PL Kastritis, ASJ Melquiond, AMJJ Bonvin, G Musco, ...
Frontiers in molecular biosciences 3, 46, 2016
BiKi Life Sciences: a New Suite for Molecular Dynamics and Related Methods in Drug Discovery
S Decherchi, G Bottegoni, A Spitaleri, W Rocchia, A Cavalli
Journal of chemical information and modeling 58 (2), 219-224, 2018
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