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Employment (3)

Istituto Italiano di Tecnologia: Genova, Liguria, IT

2014-07-01 to present | Senior Scientist (CONCEPT Lab)
Employment
Source: Self-asserted source
Walter Rocchia

Istituto Italiano di Tecnologia: Genova, Liguria, IT

2008-10-01 to 2014-06-30 | Team Leader (Drug Discovery and Development Department)
Employment
Source: Self-asserted source
Walter Rocchia

Scuola Normale Superiore: Pisa, Toscana, IT

2005-10-01 to 2008-09-30 | Research Assistant Professor (Laboratorio NEST)
Employment
Source: Self-asserted source
Walter Rocchia

Education and qualifications (2)

University of Trento: Trento, IT

1996-11 to 2000-02-18 | PhD
Education
Source: Self-asserted source
Walter Rocchia

University of Genoa: Genova, IT

1991 to 1996 (School of Engineering)
Education
Source: Self-asserted source
Walter Rocchia

Works (50 of 82)

Items per page:
Page 1 of 2

Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective

IEEE Access
2024 | Journal article
Contributors: Karthikeyan Kalyanasundaram Balasubramanian; Mirco Di Salvo; Walter Rocchia; Sergio Decherchi; Marco Crepaldi
Source: check_circle
Crossref

Locuaz: an in silico platform for protein binders optimization

Bioinformatics
2024-08-02 | Journal article
Contributors: German P Barletta; Rika Tandiana; Miguel Soler; Sara Fortuna; Walter Rocchia; Inanc Birol
Source: check_circle
Crossref

Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin

Journal of Chemical Information and Modeling
2024-06-10 | Journal article
Contributors: Stefano Bosio; Mattia Bernetti; Walter Rocchia; Matteo Masetti
Source: check_circle
Crossref

Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions

Journal of Chemical Theory and Computation
2024-03-26 | Journal article
Contributors: Rika Tandiana; German P. Barletta; Miguel Angel Soler; Sara Fortuna; Walter Rocchia
Source: check_circle
Crossref

Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets

Chemical Communications
2023 | Journal article
Contributors: Ali Douaki; Annina Stuber; Julian Hengsteler; Dmitry Momotenko; David M. Rogers; Walter Rocchia; Jonathan D. Hirst; Nako Nakatsuka; Denis Garoli
Source: check_circle
Crossref

SiteFerret: Beyond Simple Pocket Identification in Proteins

Journal of Chemical Theory and Computation
2023-08-08 | Journal article
Contributors: Luca Gagliardi; Walter Rocchia
Source: check_circle
Crossref

Biomolecular Electrostatic Phenomena: An Evergreen Field

The Journal of Physical Chemistry B
2023-05-11 | Journal article
Contributors: Wei Yang; Walter Rocchia
Source: check_circle
Crossref

Replica-exchange optimization of antibody fragments

Computational Biology and Chemistry
2023-04 | Journal article
Contributors: Miguel A. Soler; Nikola Minovski; Walter Rocchia; Sara Fortuna
Source: check_circle
Crossref

Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson–Boltzmann Framework: An Analytical Treatment

The Journal of Physical Chemistry B
2022-12-15 | Journal article
Contributors: Sergii V. Siryk; Walter Rocchia
Source: check_circle
Crossref

Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode

The Journal of Physical Chemistry B
2022-11-03 | Journal article
Contributors: Manuel Antonio Ruiz-Rodríguez; Christopher D. Cooper; Walter Rocchia; Mosè Casalegno; Yossef López de los Santos; Guido Raos
Source: check_circle
Crossref

A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven pKa Predictions in Proteins

Journal of Chemical Theory and Computation
2022-08-09 | Journal article
Contributors: Pedro B.P.S. Reis; Marco Bertolini; Floriane Montanari; Walter Rocchia; Miguel Machuqueiro; Djork-Arné Clevert
Source: check_circle
Crossref

A fast and interpretable deep learning approach for accurate electrostatics-driven pKa predictions in proteins

2022-03-23 | Preprint
Contributors: Pedro Reis; Marco Bertolini; Floriane Montanari; Walter Rocchia; Miguel Machuqueiro; Djork-Arné Clevert
Source: check_circle
Crossref

Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking

Journal of Chemical Theory and Computation
2021-11-09 | Journal article
Contributors: Nicola Scafuri; Miguel A. Soler; Andrea Spitaleri; Walter Rocchia
Source: check_circle
Crossref

pKAI: a fast and interpretable deep learning approach for accurate electrostatics-driven pKa predictions

2021-10-05 | Preprint
Contributors: Pedro Reis; Marco Bertolini; Floriane Montanari; Walter Rocchia; Miguel Machuqueiro; Djork-Arné Clevert
Source: check_circle
Crossref

Charged dielectric spheres interacting in electrolytic solution: A linearized Poisson–Boltzmann equation model

The Journal of Chemical Physics
2021-09-21 | Journal article
Contributors: Sergii V. Siryk; Artemi Bendandi; Alberto Diaspro; Walter Rocchia
Source: check_circle
Crossref

Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint

The Journal of Physical Chemistry Letters
2021-06-17 | Journal article
Contributors: Laura Riccardi; Sergio Decherchi; Walter Rocchia; Giordano Zanoni; Andrea Cavalli; Fabrizio Mancin; Marco De Vivo
Source: check_circle
Crossref

Tuning Local Hydration Enables a Deeper Understanding of Protein–Ligand Binding: The PP1-Src Kinase Case

The Journal of Physical Chemistry Letters
2021-01-14 | Journal article
Contributors: Andrea Spitaleri; Syeda R. Zia; Patrizio Di Micco; Bissan Al-Lazikani; Miguel A. Soler; Walter Rocchia
Source: check_circle
Crossref

PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations

Journal of Chemical Information and Modeling
2020-10-26 | Journal article
Contributors: Pedro B. P. S. Reis; Diogo Vila-Viçosa; Walter Rocchia; Miguel Machuqueiro
Source: check_circle
Crossref

Electrostatics and Solvation: Essential Determinants of Chromatin Compaction

2019-09-27 | Other
Contributors: A. Bendandi; S. Dante; S. Rehana Zia; A. Diaspro; W. Rocchia
Source: check_circle
Crossref

Finding Principal Paths in Data Space

IEEE Transactions on Neural Networks and Learning Systems
2019-08 | Journal article
Contributors: Marco Jacopo Ferrarotti; Walter Rocchia; Sergio Decherchi
Source: check_circle
Crossref

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

Bioinformatics
2019-04-01 | Journal article
Contributors: Sergio Decherchi; Andrea Spitaleri; John Stone; Walter Rocchia; Alfonso Valencia
Source: check_circle
Crossref

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

ChemistryOpen
2018-08 | Journal article
Contributors: Mauro Lapelosa; Oscar Burrone; Walter Rocchia
Source: check_circle
Crossref

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

Journal of Chemical Information and Modeling
2018-08-27 | Journal article
Contributors: Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli
Source: check_circle
Crossref

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

The Journal of Chemical Physics
2018-03-21 | Journal article
Contributors: Ivan Vyalov; Walter Rocchia
Source: check_circle
Crossref

Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach

Journal of Chemical Theory and Computation
2018-03-13 | Journal article
Contributors: Andrea Spitaleri; Sergio Decherchi; Andrea Cavalli; Walter Rocchia
Source: check_circle
Crossref

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

Journal of Chemical Information and Modeling
2018-02-26 | Journal article
Contributors: Sergio Decherchi; Giovanni Bottegoni; Andrea Spitaleri; Walter Rocchia; Andrea Cavalli
Source: check_circle
Crossref

Force Field Parametrization of Metal Ions from Statistical Learning Techniques

Journal of Chemical Theory and Computation
2018-01-09 | Journal article
Contributors: Francesco Fracchia; Gianluca Del Frate; Giordano Mancini; Walter Rocchia; Vincenzo Barone
Source: check_circle
Crossref

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

ACS Central Science
2017-09-27 | Journal article
Contributors: Giuseppina La Sala; Sergio Decherchi; Marco De Vivo; Walter Rocchia
Source: check_circle
Crossref

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

Analytical Biochemistry
2016 | Journal article
EID:

2-s2.0-84962209502

Contributors: Goldoni, L.; Beringhelli, T.; Rocchia, W.; Realini, N.; Piomelli, D.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

Data in Brief
2016 | Journal article
EID:

2-s2.0-84973582121

Contributors: Goldoni, L.; Beringhelli, T.; Rocchia, W.; Realini, N.; Piomelli, D.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Erratum: Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations (Scientific Reports 5: (11539) doi: 10.1038/srep11539

Scientific Reports
2016 | Journal article
EID:

2-s2.0-84966361883

Contributors: Mollica, L.; Decherchi, S.; Zia, S.R.; Gaspari, R.; Cavalli, A.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

IEEE Transactions on Neural Networks and Learning Systems
2016 | Journal article
EID:

2-s2.0-84963632294

Contributors: Decherchi, S.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

Journal of Medicinal Chemistry
2016 | Journal article
EID:

2-s2.0-84969667426

Contributors: Gaspari, R.; Rechlin, C.; Heine, A.; Bottegoni, G.; Rocchia, W.; Schwarz, D.; Bomke, J.; Gerber, H.-D.; Klebe, G.; Cavalli, A.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A<inf>2A</inf> Receptor

Journal of Chemical Theory and Computation
2016 | Journal article
EID:

2-s2.0-85006042856

Contributors: Zia, S.R.; Gaspari, R.; Decherchi, S.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

A Pipeline to Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

Journal of Chemical Information and Modeling
2015 | Journal article
EID:

2-s2.0-84945541907

Contributors: Spyrakis, F.; Benedetti, P.; Decherchi, S.; Rocchia, W.; Cavalli, A.; Alcaro, S.; Ortuso, F.; Baroni, M.; Cruciani, G.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Implicit solvent methods for free energy estimation

2015 | Journal article
EID:

2-s2.0-84921505026

Contributors: Decherchi, S.; Masetti, M.; Vyalov, I.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

Scientific Reports
2015 | Journal article
EID:

2-s2.0-84932644762

Contributors: Mollica, L.; Decherchi, S.; Zia, S.R.; Gaspari, R.; Cavalli, A.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

2015 | Journal article
EID:

2-s2.0-84923096526

Contributors: Decherchi, S.; Berteotti, A.; Bottegoni, G.; Rocchia, W.; Cavalli, A.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

2014 | Journal article
EID:

2-s2.0-84903648275

Contributors: Colmenares, J.; Galizia, A.; Ortiz, J.; Clematis, A.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

CUDA accelerated molecular surface generation

2014 | Journal article
EID:

2-s2.0-84902553505

Contributors: D'Agostino, D.; Clematis, A.; Decherchi, S.; Rocchia, W.; Milanesi, L.; Merelli, I.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Describing the conformational landscape of small organic molecules through Gaussian mixtures in dihedral space

2014 | Journal article
EID:

2-s2.0-84902199743

Contributors: Pisani, P.; Piro, P.; Decherchi, S.; Bottegoni, G.; Sona, D.; Murino, V.; Rocchia, W.; Cavalli, A.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Estimation of solvation electrostatic free energy of biomolecular systems by numerical solution of the Poisson-Boltzmann equation

Electrostatics of Soft and Disordered Matter
2014 | Book
EID:

2-s2.0-84974623385

Contributors: Colmenares, J.; Decherchi, S.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi

2014 | Journal article
Part of ISSN: 1367-4803
Source: Self-asserted source
Walter Rocchia via Crossref Metadata Search
grade
Preferred source (of 2)‎

Implicit solvent methods for free energy estimation

European Journal of Medicinal Chemistry
2014 | Journal article
EID:

2-s2.0-84906652286

Contributors: Decherchi, S.; Masetti, M.; Vyalov, I.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier
grade
Preferred source (of 2)‎

Molecular mechanics and dynamics: Numerical tools to sample the configuration space

2014 | Journal article
EID:

2-s2.0-84895477380

Contributors: Masetti, M.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

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

2014 | Journal article
Part of ISSN: 1549-9596
Source: Self-asserted source
Walter Rocchia via Crossref Metadata Search
grade
Preferred source (of 2)‎

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

2013 | Journal article
EID:

2-s2.0-84875916378

Contributors: Decherchi, S.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

A statistical mechanics handbook for protein-ligand binding simulation

2013 | Journal article
EID:

2-s2.0-84883718503

Contributors: Rocchia, W.; Bonella, S.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

Between algorithm and model: Different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution

2013 | Journal article
EID:

2-s2.0-84866315711

Contributors: Decherchi, S.; Colmenares, J.; Catalano, C.E.; Spagnuolo, M.; Alexov, E.; Rocchia, W.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier

DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

2013 | Journal article
EID:

2-s2.0-84866320593

Contributors: Sarkar, S.; Witham, S.; Zhang, J.; Zhenirovskyy, M.; Rocchia, W.; Alexov, E.
Source: Self-asserted source
Walter Rocchia via Scopus - Elsevier
Items per page:
Page 1 of 2

Peer review (32 reviews for 9 publications/grants)

Review activity for Biochemistry. (1)
Review activity for Biophysical journal. (2)
Review activity for Computers in biology and medicine. (1)
Review activity for Journal of chemical information and modeling. (7)
Review activity for Journal of chemical theory and computation : (11)
Review activity for Journal of structural biology. (1)
Review activity for PLoS computational biology. (1)
Review activity for The journal of physical chemistry letters. (3)
Review activity for The journal of physical chemistry. (5)