Walter Rocchia

Senior Researcher Tenured - Principal Investigator

Contacts

Via Enrico Melen 83, B Block, 16152 - Genova, Italy
+39 010 2897 418

About

Walter Rocchia graduated cum laude in Electronic Engineering on July 1996, with a thesis on Quantum Computing. In February 2000, he got a PhD in Electronic Devices at the University of Trento. He then was a Research Scholar at the Biochemistry Department of the Columbia University, developing models to calculate the electrostatic field generated by biological macromolecules in solution. As a consultant in the Corporate Technology Centre at Honeywell Int (NJ, USA), and then at the Bioengineering Research Centre "E. Piaggio" of University of Pisa he studied the modeling of the physical properties of actuating polymers and nanotubes in a wet environment. In 2003 he joined the Molecular Biophysics group of National Enterprise for nanoScience and Nanotechnology (NEST-INFM-CNR), at Scuola Normale Superiore of Pisa, working on molecular recognition and targeting. There, he extended his interests from algorithms for speeding up and making more accurate the calculation of the electrostatic interaction energy of biomolecules to Bioinformatic and Biostatistical techniques aimed at identifying targets and engineering molecules involved in biochemical pathways of medical relevance.

In 2008, he moved to the Drug Discovery and Development Department of the Italian Institute of Technology (IIT), working on computational approaches to ligand-protein binding free energy estimation. In 2010 he was awarded, together with the Clemson University, a NIH 5-years grant entitled: DelPhi: Software for Electrostatic Modeling of Biomolecules and Objects.

In late 2014, he created the Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab.

He is author of more than 70 publications including International Journals, book contributions and Proceedings.

IIT Publications

  • 2020
  • Bendandi A., Dante S.iit, Zia S. R., Diaspro A.iit, Rocchia W.iit
    DOI

    Chromatin Compaction Multiscale Modelling: A Complex Synergy between Theory, Simulation and Experiment

    Frontiers in Molecular Biosciences
  • 2019
  • Rios de la Rosa J.M., Pingrajai P., Pelliccia M., Spadea A., Lallana E., Gennari A.iit, Stratford I.J., Rocchia W.iit, Tirella A., Tirelli N.iit
    DOI

    Binding and Internalization in Receptor-Targeted Carriers: The Complex Role of CD44 in the Uptake of Hyaluronic Acid-Based Nanoparticles (siRNA Delivery)

    Advanced healthcare materials, vol. 8, (no. 24)
  • Ragusa E., Gastaldo P., Zunino R., Ferrarotti M.J.iit, Rocchia W.iit, Decherchi S.iit
    DOI

    Cognitive Insights into Sentic Spaces Using Principal Paths

    Cognitive Computation, vol. 11, (no. 5), pp. 656-675
  • Ferrarotti M.J.iit, Rocchia W.iit, Decherchi S.iit
    DOI

    Finding Principal Paths in Data Space

    IEEE Transactions on Neural Networks and Learning Systems, vol. 30, (no. 8), pp. 2449-2462
  • Bernetti M., Masetti M., Rocchia W.iit, Cavalli A.iit
    DOI

    Kinetics of Drug Binding and Residence Time

    Annual Review of Physical Chemistry, vol. 70, pp. 143-171
  • Bendandi A.iit, Dante S.iit, Diaspro A.iit, Rocchia W.iit

    Mesoscale bottom-up approach to the study of chromatin compaction: from single nucleosome to chromatin fibre

    Italian Celebration Day for the 50 years of CECAM
  • Bendandi A., Dante S., Diaspro A., Rocchia W.iit

    Mesoscale bottom-up approach to the study of chromatin compaction: from single nucleosome to chromatin fibre

    Computational Mathematics For Model Reduction and Predictive Modelling in Molecular and Complex Systems
  • Spitaleri A., Rocchia W.iit
    DOI

    Molecular Dynamics-based approaches describing protein binding

    Simulations in Structure-Based Drug Discovery, Publisher: Wiley-VCH
  • Decherchi S.iit, Spitaleri A.iit, Stone J., Rocchia W.iit
    DOI

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

    Bioinformatics, vol. 35, (no. 7), pp. 1241-1243
  • Reis P., Vila-Vicosa D., Rocchia W.iit, Machuqueiro M.
    DOI

    PypKa: A flexible Poisson-Boltzmann-based python API for pKa calculations

    JOINT 12th EBSA congress and 10th ICBP – IUPAP congress, July 20-24, 2019, Madrid, Spain, vol. 48, pp. 196
  • 2018
  • Rocchia W.iit

    Allosteric communication networks in proteins revealed through pocket Crosstalk analysis

    256th ACS National Meeting
  • Decherchi S.iit, Bottegoni G., Spitaleri A.iit, Rocchia W.iit, Cavalli A.iit
    DOI

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

    Journal of Chemical Information and Modeling, vol. 58, (no. 2), pp. 219-224
  • Decherchi S.iit, Bottegoni G., Spitaleri A.iit, Rocchia W.iit, Cavalli A.iit
    DOI

    Erratum: Addendum to BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery (Journal of chemical information and modeling (2018) 58 2 (219-224))

    Journal of Chemical Information and Modeling, vol. 58, (no. 8)
  • Spitaleri A.iit, Decherchi S.iit, Cavalli A.iit, Rocchia W.iit
    DOI

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

    Journal of Chemical Theory and Computation, vol. 14, (no. 3), pp. 1727-1736
  • Fracchia F., Del Frate G., Mancini G., Rocchia W.iit, Barone V.
    DOI

    Force Field Parametrization of Metal Ions from Statistical Learning Techniques

    Journal of Chemical Theory and Computation, vol. 14, (no. 1), pp. 255-273
  • Vyalov I.iit, Rocchia W.iit
    DOI

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

    Journal of Chemical Physics, vol. 148, (no. 11)
  • Reis P., Vila-Viçosa D., Rocchia W.iit, Machuqueiro M.
    DOI

    PypKa: a python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

    FROM MOLECULES TO NETWORKS
  • Lapelosa M.iit, Burrone O., Rocchia W.iit
    DOI

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

    ChemistryOpen, vol. 7, (no. 8), pp. 604-610
  • 2017
  • La Sala G.iit, Decherchi S.iit, De Vivo M.iit, Rocchia W.iit
    DOI

    Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

    ACS Central Science, vol. 3, (no. 9), pp. 949-960
  • Ferrarotti M. J., Decherchi S.iit, Rocchia W.iit
    DOI

    Distributed Kernel K-Means for Large Scale Clustering

    International Conference on Artificial Intelligence and Soft Computing
  • Decherchi S.iit, Rocchia W.iit
    DOI

    Import vector domain description: A kernel logistic one-class learning algorithm

    IEEE Transactions on Neural Networks and Learning Systems, vol. 28, (no. 7), pp. 1722-1729
  • Rocchia W.iit

    MD-binding: Enabling fully dynamic simulation of binding for real-world drug-target systems

    254th ACS National Meeting Washington
  • 2016
  • Goldoni L.iit, Beringhelli T., Rocchia W.iit, Realini N.iit, Piomelli D.iit
    DOI

    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

    Data in Brief, vol. 8, pp. 387-393
  • Goldoni L.iit, Beringhelli T., Rocchia W.iit, Realini N.iit, Piomelli D.iit
    DOI

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

    Analytical Biochemistry, vol. 501, pp. 26-34
  • Spiliotopoulos D., Kastritis P.L., Melquiond A.S.J., Bonvin A.M.J.J., Musco G., Rocchia W.iit, Spitaleri A.iit
    DOI

    dMM-PBSA: A new HADDOCK scoring function for protein-peptide docking

    Frontiers in Molecular Biosciences, vol. 3, (no. AUG)
  • Mollica L., Decherchi S.iit, Zia S.R., Gaspari R., Cavalli A.iit, Rocchia W.iit
    DOI

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

    Scientific Reports, vol. 6
  • Gaspari R.iit, Rechlin C., Heine A., Bottegoni G.iit, Rocchia W.iit, Schwarz D., Bomke J., Gerber H.-D., Klebe G., Cavalli A.iit
    DOI

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

    Journal of Medicinal Chemistry, vol. 59, (no. 9), pp. 4245-4256
  • Zia S.R.iit, Gaspari R.iit, Decherchi S.iit, Rocchia W.iit
    DOI

    Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor

    Journal of Chemical Theory and Computation, vol. 12, (no. 12), pp. 6049-6061
  • 2015
  • Spyrakis F., Benedetti P., Decherchi S.iit, Rocchia W.iit, Cavalli A.iit, Alcaro S., Ortuso F., Baroni M., Cruciani G.
    DOI

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

    Journal of Chemical Information and Modeling, vol. 55, (no. 10), pp. 2256-2274
  • Decherchi S.iit, Rocchia W.iit
    DOI

    Building and Analyzing Molecular Surfaces: A Tutorial on NanoShaper

    Computational Electrostatics for Biological Applications, Publisher: Springer International Publishing
  • Decherchi S.iit, Masetti M., Vyalov I.iit, Rocchia W.iit
    DOI

    Implicit solvent methods for free energy estimation

    European Journal of Medicinal Chemistry, vol. 91, pp. 27-42
  • Mollica L.iit, Decherchi S.iit, Zia S.R.iit, Gaspari R.iit, Cavalli A.iit, Rocchia W.iit
    DOI

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

    Scientific Reports, vol. 5
  • Decherchi S.iit, Berteotti A.iit, Bottegoni G.iit, Rocchia W.iit, Cavalli A.iit
    DOI

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

    Nature Communications, vol. 6
  • Neshich G., Neshich I. A.P., Moraes F., Salim J. A., Borro L., Yano I. H., Mazoni I., Jardine J. G., Rocchia W.iit
    DOI

    Using Structural and Physical–Chemical Parameters to Identify, Classify, and Predict Functional Districts in Proteins—The Role of Electrostatic Potential

    Computational Electrostatics for Biological Applications, Publisher: Springer International Publishing
  • 2014
  • Colmenares J.iit, Galizia A., Ortiz J.iit, Clematis A., Rocchia W.iit
    DOI

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

    BioMed Research International, vol. 2014
  • D'Agostino D., Clematis A., Decherchi S.iit, Rocchia W.iit, Milanesi L., Merelli I.
    DOI

    CUDA accelerated molecular surface generation

    Concurrency Computation Practice and Experience, vol. 26, (no. 10), pp. 1819-1831
  • Pisani P.iit, Piro P.iit, Decherchi S.iit, Bottegoni G.iit, Sona D.iit, Murino V.iit, Rocchia W.iit, Cavalli A.iit
    DOI

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

    Journal of Chemical Theory and Computation, vol. 10, (no. 6), pp. 2557-2568
  • Colmenares J.iit, Decherchi S.iit, Rocchia W.iit
    DOI

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

    Electrostatics of Soft and Disordered Matter, pp. 299-314, Publisher: Pan Stanford Publishing Pte. Ltd.
  • Colmenares J., Ortiz J.iit, Rocchia W.
    DOI

    GPU linear and non-linear poisson-boltzmann solver module for delphi

    Bioinformatics, vol. 30, (no. 4), pp. 569-570
  • Masetti M., Rocchia W.iit
    DOI

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

    Frontiers in Bioscience - Landmark, vol. 19, (no. 4), pp. 578-604
  • Patel J.S.iit, Berteotti A.iit, Ronsisvalle S., Rocchia W.iit, Cavalli A.iit
    DOI

    Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5

    Journal of Chemical Information and Modeling, vol. 54, (no. 2), pp. 470-480
  • 2013
  • Decherchi S.iit, Rocchia W.iit
    DOI

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

    PLoS ONE, vol. 8, (no. 4)
  • Rocchia W.iit, Bonella S.

    A statistical mechanics handbook for protein-ligand binding simulation

    Frontiers in Bioscience - Scholar, vol. 5 S, (no. 2), pp. 478-495
  • Decherchi S.iit, Colmenares J.iit, Catalano C.E., Spagnuolo M., Alexov E., Rocchia W.iit
    DOI

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

    Communications in Computational Physics, vol. 13, (no. 1), pp. 61-89
  • Sarkar S., Witham S., Zhang J., Zhenirovskyy M., Rocchia W.iit, Alexov E.
    DOI

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

    Communications in Computational Physics, vol. 13, (no. 1), pp. 269-284
  • Fu J., Bottegoni G., Sasso O., Bertorelli R.iit, Rocchia W.iit, Masetti M., Guijarro A., Lodola A., Armirotti A.iit, Garau G.iit, Bandiera T.iit, Reggiani A.iit, Mor M., Cavalli A.iit, Piomelli D.
    DOI

    Erratum: A catalytically silent FAAH-1 variant drives anandamide transport in neurons (Nature Neuroscience (2012) 15 (64-69))

    Nature Neuroscience, vol. 16, (no. 12)
  • Colmenares J.iit, Ortiz J.iit, Decherchi S.iit, Fijany A., Rocchia W.iit
    DOI

    Solving the linearized Poisson-Boltzmann equation on GPUs using CUDA

    Proceedings of the 2013 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2013, pp. 420-426
  • Wang L., Zhang Z., Rocchia W.iit, Alexov E.
    DOI

    Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants

    Communications in Computational Physics, vol. 13, (no. 1), pp. 13-30
  • 2012
  • Fu J., Bottegoni G.iit, Sasso O.iit, Bertorelli R.iit, Rocchia W.iit, Masetti M.iit, Guijarro A., Lodola A., Armirotti A.iit, Garau G.iit, Bandiera T.iit, Reggiani A.iit, Mor M., Cavalli A.iit, Piomelli D.iit
    DOI

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

    Nature Neuroscience, vol. 15, (no. 1), pp. 64-69
  • Bottegoni G.iit, Rocchia W.iit, Cavalli A.iit
    DOI

    Application of conformational clustering in protein-ligand docking

    Methods in molecular biology (Clifton, N.J.), vol. 819, pp. 169-186
  • D'Agostino D., Decherchi S.iit, Galizia A., Colmenares J.iit, Quarati A., Rocchia W.iit, Clematis A.
    DOI

    CUDA accelerated blobby molecular surface generation

    Lecture Notes in Computer Science, vol. 7203 LNCS, (no. PART 1), pp. 347-356
  • Rocchia W.iit, Masetti M., Cavalli A.iit
    DOI

    Enhanced Sampling Methods in Drug Design

    RSC Drug Discovery Series, pp. 273-301
  • Piro P.iit, Pisani P.iit, Bottegoni G.iit, Sona D.iit, Rocchia W.iit, Cavalli A.iit, Murino V.iit

    Fitting and simplification of mixtures for clustering conformational populations of small organic molecules

    International Conference on Chemical and Biological Engineering
  • 2011
  • Patel J.S.iit, Branduardi D.iit, Masetti M.iit, Rocchia W.iit, Cavalli A.iit
    DOI

    Insights into ligand-protein binding from local mechanical response

    Journal of Chemical Theory and Computation, vol. 7, (no. 10), pp. 3368-3378
  • Bottegoni G.iit, Rocchia W.iit, Rueda M., Abagyan R., Cavalli A.iit
    DOI

    Systematic exploitation of multiple receptor conformations for virtual ligand screening

    PLoS ONE, vol. 6, (no. 5)
  • 2009
  • Di Fenza A., Rocchia W.iit, Tozzini V.
    DOI

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

    Proteins: Structure, Function and Genetics, vol. 76, (no. 4), pp. 946-958
  • Bonella S., Rocchia W.iit, Amat P., Nifosi R., Tozzini V.
    DOI

    SDPhound, a mutual information-based method to investigate specificity-determining positions

    Algorithms, vol. 2, (no. 2), pp. 764-789
  • 2008
  • Mazzoldi A., Tesconi M., Tognetti A., Rocchia W.iit, Vozzi G., Pioggia G., Ahluwalia A., De Rossi D.
    DOI

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

    Materials Science and Engineering C, vol. 28, (no. 7), pp. 1057-1064
  • 2007
  • Rocchia W.iit, Neshich G.

    Electrostatic potential calculation for biomolecules - Creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures

    Genetics and Molecular Research, vol. 6, (no. 4), pp. 923-936
  • Bizzarri R., Nifosi R., Abbruzzetti S., Rocchia W.iit, Guidi S., Arosio D., Garau G., Campanini B., Grandi E., Ricci F., Viappiani C., Beltram F.
    DOI

    Green fluorescent protein ground states: The influence of a second protonation site near the chromophore

    Biochemistry, vol. 46, (no. 18), pp. 5494-5504
  • Bizzarri R., Nifosi R., Abbruzzetti S., Rocchia W.iit, Guidi S., Arosio D., Garau G.iit, Campanini B., Grandi E., Ricci F., Viappiani C., Beltram F.

    Thermodynamic and kinetic characterization of protonation exchanges in GFPs: a way to mutants with tailored optical properties

    Biophysical Journal
  • 2006
  • Bottegoni G., Rocchia W., Recanatini M., Cavalli A.
    DOI

    AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets

    Bioinformatics, vol. 22, (no. 14)
  • Tozzini V., Rocchia W., McCammon J.A.
    DOI

    Mapping all-atom models onto one-bead coarse-grained models: General properties and applications to a minimal polypeptide model

    Journal of Chemical Theory and Computation, vol. 2, (no. 3), pp. 667-673
  • Giordano S., Rocchia W.
    DOI

    Predicting the dielectric nonlinearity of anisotropic composite materials via tensorial analysis

    Journal of Physics Condensed Matter, vol. 18, (no. 47), pp. 10585-10599
  • 2005
  • Mosca R., Queirolo F., Rocchia W., Tonelli F.

    Designed simulation (DOE) of complex systems: New frontiers in using neural networks for R.S. research part two: Assessment of the new approach

    Summer Computer Simulation Conference 2005, SCSC 2005, Part of the 2005 Summer Simulation Multiconference, SummerSim 2005, pp. 450-455
  • Rocchia W.
    DOI

    Poisson-Boltzmann equation boundary conditions for biological applications

    Mathematical and Computer Modelling, vol. 41, (no. 10), pp. 1109-1118
  • Giordano S., Rocchia W.
    DOI

    Shape-dependent effects of dielectrically nonlinear inclusions in heterogeneous media

    Journal of Applied Physics, vol. 98, (no. 10)
  • 2004
  • Rocchia W., Zoppi L., Colombo L.
    DOI

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

    Computational Materials Science, vol. 30, (no. 1-2 SPEC ISS.), pp. 150-154
  • Pioggia G., Ahluwalia A., Carpi F., Marchetti A., Ferro M., Rocchia W., De Rossi D.
    DOI

    FACE: Facial Automaton for Conveying Emotions

    Applied Bionics and Biomechanics, vol. 1, (no. 2), pp. 91-100
  • Neshich G., Rocchia W., Mancini A.L., Yamagishi M.E.B., Kuser P.R., Fileto R., Baudet C., Pinto I.P., Montagner A.J., Palandrani J.F., Krauchenco J.N., Torres R.C., Souza S., Togawa R.C., Higa R.H.
    DOI

    JavaProtein Dossier: A novel web-based data visualization tool for comprehensive analysis of protein structure

    Nucleic Acids Research, vol. 32, (no. WEB SERVER ISS.)
  • Lorussi F., Rocchia W., Scilingo E.P., Tognetti A., De Rossi D.
    DOI

    Wearable, redundant fabric-based sensor arrays for reconstruction of body segment posture

    IEEE Sensors Journal, vol. 4, (no. 6), pp. 807-818
  • 2003
  • Rocchia W., Mazzoldi A., Serra G., De Rossi D.
    DOI

    Exploiting conducting polymer fiber radial expansion for bioinspired actuation

    Proceedings of SPIE - The International Society for Optical Engineering, vol. 5051, pp. 453-457
  • 2002
  • Rocchia W., Sridharan S., Nicholls A., Alexov E., Chiabrera A., Honig B.
    DOI

    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

    Journal of Computational Chemistry, vol. 23, (no. 1), pp. 128-137
  • 2001
  • De Rossi D., Lorussi F., Mazzoldi A., Rocchia W., Scilingo E.P.
    DOI

    A strain amplified electroactive polymer actuator for haptic interfaces

    Proceedings of SPIE - The International Society for Optical Engineering, vol. 4329, pp. 43-53
  • Rocchia W., Alexov E., Honig B.
    DOI

    Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions

    Journal of Physical Chemistry B, vol. 105, (no. 28), pp. 6507-6514
  • Bianco B., Moggia E., Giordano S., Rocchia W., Chiabrera A.

    Friction and noise in quantum mechanics: A model for the interactions between a system and a thermal bath

    Nuovo Cimento della Societa Italiana di Fisica B, vol. 116, (no. 2), pp. 155-167
  • 1996
  • Bonfiglio A., Parodi M.T., Di Zitti E., Ricci D., Rocchia W., Bianco B., Chiabrera A., Ruggeri G.

    Experimental study on the structural and electrical properties of pyrrole derivatives Langmuir-Blodgett films

    Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings, vol. 5, pp. 2067-2068

Scientific Talks

  • 2018
  • Rocchia W.iit

    Allosteric communication networks in proteins revealed through pocket Crosstalk analysis

  • 2017
  • Rocchia W.iit

    MD-binding: Enabling fully dynamic simulation of binding for real-world drug-target systems