82 publications found

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  • 2021
    Spitaleri A.iit , Garoli D.iit , Schutte M. , Lehrach H. , *Rocchia W.iit , De Angelis F.iit

    Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

    Nano Research, vol. 14, (no. 1), pp. 328-333
    Article
  • 2021
    Ochoa R. , Soler M.A.iit , Laio A. , Cossio P.

    PARCE: Protocol for Amino acid Refinement through Computational Evolution

    Computer Physics Communications, vol. 260
    Article
  • 2021
    Spitaleri A.iit , Zia S.R.iit , Di Micco P. , Al-Lazikani B. , Soler M.A.iit , *Rocchia W.iit

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

    Journal of Physical Chemistry Letters, pp. 49-58
    Article
  • 2020
    Sturla F. , Piatti F. , Jaworek M. , Lucherini F. , Pluchinotta F.R. , Siryk S.V.iit , Giese D. , Vismara R. , Tasca G. , Menicanti L. , Redaelli A. , Lombardi M.

    4D Flow MRI hemodynamic benchmarking of surgical bioprosthetic valves

    Magnetic Resonance Imaging, vol. 68, pp. 18-29
    Article
  • 2020
    Krasnoschok M. , Pata V. , Siryk S.V.iit , Vasylyeva N.

    A subdiffusive Navier–Stokes–Voigt system

    Physica D: Nonlinear Phenomena, vol. 409
    Article
  • 2020
    Bendandi A.iit , Dante S.iit , Zia S.R. , Diaspro A.iit , *Rocchia W.iit

    Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

    Frontiers in Molecular Biosciences, vol. 7
    Review
  • 2020
    Bendandi A.iit , Dante S. , Diaspro A.iit , Rocchia W.iit

    Electrostatic Interactions in Nucleosomes: a Comprehensive Analysis

    Remote BioExcel Winter School on Biomolecular Simulations
    Poster
  • 2020
    Krasnoschok M. , Pata V. , Siryk S.V.iit , Vasylyeva N.

    Equivalent definitions of Caputo derivatives and applications to subdiffusion equations

    Dynamics of Partial Differential Equations, vol. 17, (no. 4), pp. 383-402
    Article
  • 2020
    Huang J.-A.iit , Mousavi M.Z.iit , Giovannini G.iit , Zhao Y.iit , Hubarevich A.iit , Soler M.A.iit , Rocchia W.iit , Garoli D.iit , De Angelis F.iit

    Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot

    Angewandte Chemie - International Edition, vol. 59, (no. 28), pp. 11423-11431
    Article
  • 2020
    Reis P.B.P.S.iit , Vila-Vicosa D. , *Rocchia W.iit , Machuqueiro M.

    PypKA: A flexible python module for poisson-Boltzmann-based pKa calculations

    Journal of Chemical Information and Modeling, vol. 60, (no. 10), pp. 4442-4448
    Article
  • 2020
    Bendandi A.iit , Patelli A.S. , Diaspro A.iit , *Rocchia W.iit

    The role of histone tails in nucleosome stability: An electrostatic perspective

    Computational and Structural Biotechnology Journal, vol. 18, pp. 2799-2809
    Article
  • 2019
    Soler M.A.iit , Medagli B. , Semrau M.S. , Storici P. , Bajc G. , De Marco A. , Laio A. , Fortuna S.

    A consensus protocol for the: In silico optimisation of antibody fragments

    Chemical Communications, vol. 55, (no. 93), pp. 14043-14046
    Article
  • 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

    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)
    Article
  • 2019
    Ragusa E. , Gastaldo P. , Zunino R. , Ferrarotti M.J.iit , Rocchia W.iit , Decherchi S.iit

    Cognitive Insights into Sentic Spaces Using Principal Paths

    Cognitive Computation, vol. 11, (no. 5), pp. 656-675
    Article
  • 2019
    Ferrarotti M.J.iit , *Rocchia W.iit , Decherchi S.iit

    Finding Principal Paths in Data Space

    IEEE Transactions on Neural Networks and Learning Systems, vol. 30, (no. 8), pp. 2449-2462
    Article
  • 2019
    *Soler M. A.iit

    In silico design of protein binders for medical applications

    INTEGRATIVE APPROACHES TO PROTEIN FOLDING & AGGREGATION
    Abstract Report
  • 2019
    Bernetti M. , Masetti M. , *Rocchia W.iit , Cavalli A.iit

    Kinetics of Drug Binding and Residence Time

    Annual Review of Physical Chemistry, vol. 70, pp. 143-171
    Review
  • 2019
    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
    Poster
  • 2019
    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
    Poster
  • 2019
    Spitaleri A. , *Rocchia W.iit

    Molecular Dynamics-based approaches describing protein binding

    Simulations in Structure-Based Drug Discovery, Publisher: Wiley-VCH
    Book Chapter
  • 2019
    Decherchi S.iit , Spitaleri A.iit , Stone J. , *Rocchia W.iit

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

    Bioinformatics, vol. 35, (no. 7), pp. 1241-1243
    Article
  • 2019
    Reis P. , Vila-Vicosa D. , *Rocchia W.iit , Machuqueiro M.

    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
    Conference Paper
  • 2019
    Gagliardi L.iit , Pierre-Louis O.

    The nonequilibrium crystallization force

    Europhysics Letters, vol. 127, (no. 5)
    Article
  • 2018
    *Rocchia W.iit

    Allosteric communication networks in proteins revealed through pocket Crosstalk analysis

    256th ACS National Meeting
    Abstract Report
  • 2018
    Decherchi S.iit , Bottegoni G. , Spitaleri A.iit , *Rocchia W.iit , *Cavalli A.iit

    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
    Article