Walter Rocchia : rechercher sur Z-Library

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1

The Role of Histone Tails in Nucleosome Stability: an Electrostatic Perspective

Bendandi, Artemi, Patelli, Alessandro S., Diaspro, Alberto, Rocchia, Walter

Journal:

Computational and Structural Biotechnology Journal

Année:

2020

Fichier:

PDF, 4.53 MB

2020

2

Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery

Decherchi, Sergio, Bottegoni, Giovanni, Spitaleri, Andrea, Rocchia, Walter, Cavalli, Andrea

Journal:

Journal of Chemical Information and Modeling

Année:

2018

Langue:

english

Fichier:

PDF, 325 KB

english, 2018

3

Computational Electrostatics for Biological Applications ||

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 11.25 MB

english, 2015

4

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

Decherchi, Sergio, Berteotti, Anna, Bottegoni, Giovanni, Rocchia, Walter, Cavalli, Andrea

Journal:

Nature Communications

Année:

2015

Langue:

english

Fichier:

PDF, 2.01 MB

english, 2015

5

BiKi Life Sciences: a New Suite for Molecular Dynamics and Related Methods in Drug Discovery

Decherchi, Sergio, Bottegoni, Giovanni, spitaleri, andrea, Rocchia, Walter, Cavalli, Andrea

Journal:

Journal of Chemical Information and Modeling

Année:

2018

Langue:

english

Fichier:

PDF, 501 KB

english, 2018

6

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 geometric objects

Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig

Journal:

Journal of Computational Chemistry

Année:

2002

Langue:

english

Fichier:

PDF, 210 KB

english, 2002

7

Electroactive carbon nanotube actuators: Soft-lithographic fabrication and electro-chemical modelling

Alberto Mazzoldi, Mario Tesconi, Alessandro Tognetti, Walter Rocchia, Giovanni Vozzi, Giovanni Pioggia, Arti Ahluwalia, Danilo De Rossi

Journal:

Materials Science and Engineering: C

Année:

2008

Langue:

english

Fichier:

PDF, 915 KB

english, 2008

8

Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition

Armida Di Fenza, Walter Rocchia, Valentina Tozzini

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 829 KB

english, 2009

9

Green Fluorescent Protein Ground States: The Influence of a Second Protonation Site near the Chromophore †,‡

Bizzarri, Ranieri, Nifosì, Riccardo, Abbruzzetti, Stefania, Rocchia, Walter, Guidi, Sara, Arosio, Daniele, Garau, Gianpiero, Campanini, Barbara, Grandi, Elena, Ricci, Fernanda, Viappiani, Cristiano, B

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 327 KB

english, 2007

10

Combined atomistic and continuum methods to map electric properties of nanostructured carbon films

Walter Rocchia, Laura Zoppi, Luciano Colombo

Journal:

Computational Materials Science

Année:

2004

Langue:

english

Fichier:

PDF, 661 KB

english, 2004

11

A catalytically silent FAAH-1 variant drives anandamide transport in neurons

Fu, Jin, Bottegoni, Giovanni, Sasso, Oscar, Bertorelli, Rosalia, Rocchia, Walter, Masetti, Matteo, Guijarro, Ana, Lodola, Alessio, Armirotti, Andrea, Garau, Gianpiero, Bandiera, Tiziano, Reggiani, Ang

Journal:

Nature Neuroscience

Année:

2011

Langue:

english

Fichier:

PDF, 808 KB

english, 2011

12

Insights into Ligand–Protein Binding from Local Mechanical Response

Patel, Jagdish Suresh, Branduardi, Davide, Masetti, Matteo, Rocchia, Walter, Cavalli, Andrea

Journal:

Journal of Chemical Theory and Computation

Année:

2011

Langue:

english

Fichier:

PDF, 4.27 MB

english, 2011

13

Describing the Conformational Landscape of Small Organic Molecules through Gaussian Mixtures in Dihedral Space

Pisani, Pasquale, Piro, Paolo, Decherchi, Sergio, Bottegoni, Giovanni, Sona, Diego, Murino, Vittorio, Rocchia, Walter, Cavalli, Andrea

Journal:

Journal of Chemical Theory and Computation

Année:

2014

Langue:

english

Fichier:

PDF, 2.71 MB

english, 2014

14

Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

Patel, Jagdish Suresh, Berteotti, Anna, Ronsisvalle, Simone, Rocchia, Walter, Cavalli, Andrea

Journal:

Journal of Chemical Information and Modeling

Année:

2014

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2014

15

Mapping All-Atom Models onto One-Bead Coarse-Grained Models: General Properties and Applications to a Minimal Polypeptide Model

Tozzini, Valentina, Rocchia, Walter, McCammon, J. Andrew

Journal:

Journal of Chemical Theory and Computation

Année:

2006

Langue:

english

Fichier:

PDF, 342 KB

english, 2006

16

Shape-dependent effects of dielectrically nonlinear inclusions in heterogeneous media

Giordano, Stefano, Rocchia, Walter

Journal:

Journal of Applied Physics

Année:

2005

Langue:

english

Fichier:

PDF, 838 KB

english, 2005

17

Computational Electrostatics for Biological Applications || State-of-the-Art and Perspectives of Geometric and Implicit Modeling for Molecular Surfaces

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2015

18

Computational Electrostatics for Biological Applications || The Representation of Electrostatics for Biological Molecules

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 434 KB

english, 2015

19

Computational Electrostatics for Biological Applications || Electrostatics Models for Biology

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 298 KB

english, 2015

20

Computational Electrostatics for Biological Applications || Evaluation of Protein Electrostatic Potential from Molecular Dynamics Simulations in the Presence of Exogenous Electric Fields: The Case Study of Myoglobin

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 929 KB

english, 2015

21

CUDA accelerated molecular surface generation

D'Agostino, Daniele, Clematis, Andrea, Decherchi, Sergio, Rocchia, Walter, Milanesi, Luciano, Merelli, Ivan

Journal:

Concurrency and Computation: Practice and Experience

Année:

2014

Langue:

english

Fichier:

PDF, 759 KB

english, 2014

22

Corrigendum: A catalytically silent FAAH-1 variant drives anandamide transport in neurons

Fu, Jin, Bottegoni, Giovanni, Sasso, Oscar, Bertorelli, Rosalia, Rocchia, Walter, Masetti, Matteo, Guijarro, Ana, Lodola, Alessio, Armirotti, Andrea, Garau, Gianpiero, Bandiera, Tiziano, Reggiani, Ang

Journal:

Nature Neuroscience

Année:

2013

Langue:

english

Fichier:

PDF, 87 KB

english, 2013

23

Implicit solvent methods for free energy estimation

Decherchi, Sergio, Masetti, Matteo, Vyalov, Ivan, Rocchia, Walter

Journal:

European Journal of Medicinal Chemistry

Année:

2015

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2015

24

Computational Electrostatics for Biological Applications || Classical Density Functional Theory of Ionic Solutions

Rocchia, Walter, Spagnuolo, Michela

Année:

2015

Langue:

english

Fichier:

PDF, 483 KB

english, 2015

25

A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation

Colmenares, José, Galizia, Antonella, Ortiz, Jesús, Clematis, Andrea, Rocchia, Walter

Journal:

BioMed Research International

Année:

2014

Langue:

english

Fichier:

PDF, 613 KB

english, 2014

26

A pipeline to enhance ligand virtual screening: integrating Molecular Dynamics and FLAP

spyrakis, francesca, Benedetti, Paolo, Decherchi, Sergio, Rocchia, Walter, Cavalli, Andrea, Alcaro, Stefano, Ortuso, Francesco, Baroni, Massimo, Cruciani, Gabriele

Journal:

Journal of Chemical Information and Modeling

Année:

2015

Langue:

english

Fichier:

PDF, 2.54 MB

english, 2015

27

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

Gaspari, Roberto, Rechlin, Chris, Heine, Andreas, Bottegoni, Giovanni, Rocchia, Walter, Schwarz, Daniel, Bomke, Joerg, Gerber, Hans-Dieter, Klebe, Gerhard, Cavalli, Andrea

Journal:

Journal of Medicinal Chemistry

Année:

2015

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2015

28

SPIE Proceedings [SPIE Smart Structures and Materials - San Diego, CA (Sunday 2 March 2003)] Smart Structures and Materials 2003: Electroactive Polymer Actuators and Devices (EAPAD) - Exploiting conducting polymer fiber radial expansion for bio-inspired actuation

Rocchia, Walter, Mazzoldi, Alberto, Serra, Giorgio, De Rossi, Danilo, Bar-Cohen, Yoseph

Année:

2003

Langue:

english

Fichier:

PDF, 114 KB

english, 2003

29

A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using quantitative nuclear magnetic resonance

Goldoni, Luca, Beringhelli, Tiziana, Rocchia, Walter, Realini, Natalia, Piomelli, Daniele

Journal:

Analytical Biochemistry

Année:

2016

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2016

30

Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm

Decherchi, Sergio, Rocchia, Walter

Journal:

IEEE Transactions on Neural Networks and Learning Systems

Année:

2016

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2016

31

FACE: facial automaton for conveying emotions

Pioggia, Giovanni, Ahluwalia, Arti, Carpi, Federico, Marchetti, Andrea, Ferro, Marcello, Rocchia, Walter, Rossi, Danilo De

Journal:

Applied Bionics and Biomechanics

Année:

2004

Langue:

english

Fichier:

PDF, 371 KB

english, 2004

32

SPIE Proceedings [SPIE SPIE's 8th Annual International Symposium on Smart Structures and Materials - Newport Beach, CA, USA (Sunday 4 March 2001)] Smart Structures and Materials 2001: Electroactive Polymer Actuators and Devices - Strain-amplified electroactive polymer actuator for haptic interfaces

De Rossi, Danilo, Bar-Cohen, Yoseph, Lorussi, Federico, Mazzoldi, Alberto, Rocchia, Walter, Pasquale Scilingo, Enzo

Année:

2001

Langue:

english

Fichier:

PDF, 187 KB

english, 2001

33

Absolute nutrient concentration measurements in cell culture media: 1H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches

Goldoni, Luca, Beringhelli, Tiziana, Rocchia, Walter, Realini, Natalia, Piomelli, Daniele

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 816 KB

english, 2016

34

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

Mollica, Luca, Decherchi, Sergio, Zia, Syeda Rehana, Gaspari, Roberto, Cavalli, Andrea, Rocchia, Walter

Journal:

Scientific Reports

Année:

2015

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2015

35

Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A 2A Receptor

Zia, Syeda Rehana, Gaspari, Roberto, Decherchi, Sergio, Rocchia, Walter

Journal:

Journal of Chemical Theory and Computation

Année:

2016

Langue:

english

Fichier:

PDF, 7.67 MB

english, 2016

36

Erratum: Corrigendum: Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

Mollica, Luca, Decherchi, Sergio, Zia, Syeda Rehana, Gaspari, Roberto, Cavalli, Andrea, Rocchia, Walter

Journal:

Scientific Reports

Année:

2016

Langue:

english

Fichier:

PDF, 462 KB

english, 2016

37

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

La Sala, Giuseppina, Decherchi, Sergio, De Vivo, Marco, Rocchia, Walter

Journal:

ACS Central Science

Année:

2017

Langue:

english

Fichier:

PDF, 4.28 MB

english, 2017

38

Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants

Wang, Lin, Zhang, Zhe, Rocchia, Walter, Alexov, Emil

Journal:

Communications in Computational Physics

Année:

2013

Langue:

english

Fichier:

PDF, 829 KB

english, 2013

39

Force Field Parametrization of Metal Ions From Statistical Learning Techniques

Fracchia, Francesco, Del Frate, Gianluca, Mancini, Giordano, Rocchia, Walter, Barone, Vincenzo

Journal:

Journal of Chemical Theory and Computation

Année:

2017

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2017

40

Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

Decherchi, Sergio, Colmenares, Jose, Catalano, Chiara Eva, Spagnuolo, Michela, Alexov, Emil, Rocchia, Walter

Journal:

Communications in Computational Physics

Année:

2013

Langue:

english

Fichier:

PDF, 988 KB

english, 2013

41

Fast dynamic docking guided by adaptive electrostatic bias: the MD-Binding approach

spitaleri, andrea, Decherchi, Sergio, Cavalli, Andrea, Rocchia, Walter

Journal:

Journal of Chemical Theory and Computation

Année:

2018

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2018

42

Including diverging electrostatic potential in 3D-RISM theory: The charged wall case

Vyalov, Ivan, Rocchia, Walter

Journal:

The Journal of Chemical Physics

Année:

2018

Langue:

english

Fichier:

PDF, 835 KB

english, 2018

43

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

Bottegoni, Giovanni, Rocchia, Walter, Rueda, Manuel, Abagyan, Ruben, Cavalli, Andrea, Gasset, Maria

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2011

44

A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

Decherchi, Sergio, Rocchia, Walter, Lorenz, Chris

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2013

45

FACE: Facial Automaton for Conveying Emotions

Pioggia, Giovanni, Ahluwalia, Arti, Carpi, Federico, Marchetti, Andrea, Ferro, Marcello, Rocchia, Walter, De Rossi, Danilo

Journal:

Applied Bionics and Biomechanics

Année:

2004

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2004

46

SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions

Bonella, Sara, Rocchia, Walter, Amat, Pietro, Nifosí, Riccardo, Tozzini, Valentina

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 1.42 MB

english, 2009

47

dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking

Spiliotopoulos, Dimitrios, Kastritis, Panagiotis L., Melquiond, Adrien S. J., Bonvin, Alexandre M. J. J., Musco, Giovanna, Rocchia, Walter, Spitaleri, Andrea

Journal:

Frontiers in Molecular Biosciences

Année:

2016

Langue:

english

Fichier:

PDF, 955 KB

english, 2016

48

A statistical mechanics handbook for protein-ligand binding simulation

Rocchia, Walter

Journal:

Frontiers in Bioscience

Année:

2013

Langue:

english

Fichier:

PDF, 2.06 MB

english, 2013

49

NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems

Decherchi, Sergio, Spitaleri, Andrea, Stone, John, Rocchia, Walter, Valencia, Alfonso

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.21 MB

english, 2018

50

Specific Residue Interactions Regulate the Binding of Dengue Antigens to Broadly Neutralizing EDE Antibodies

Lapelosa, Mauro, Burrone, Oscar, Rocchia, Walter

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.35 MB

english, 2018