64 publications found

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  • 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
    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
    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. , Diaspro A. , *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
  • 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
  • 2018
    Decherchi S.iit , Bottegoni G. , Spitaleri A.iit , *Rocchia W.iit , Cavalli A.iit

    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)
    Erratum
  • 2018
    Spitaleri A.iit , Decherchi S.iit , *Cavalli A.iit , *Rocchia W.iit

    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
    Article
  • 2018
    Fracchia F. , Del Frate G. , Mancini G. , Rocchia W.iit , Barone V.

    Force Field Parametrization of Metal Ions from Statistical Learning Techniques

    Journal of Chemical Theory and Computation, vol. 14, (no. 1), pp. 255-273
    Article
  • 2018
    Vyalov I.iit , *Rocchia W.iit

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

    Journal of Chemical Physics, vol. 148, (no. 11)
    Article
  • 2018
    Reis P. , Vila-Viçosa D. , *Rocchia W.iit , Machuqueiro M.

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

    FROM MOLECULES TO NETWORKS
    Conference Paper
  • 2018
    Lapelosa M.iit , Burrone O. , *Rocchia W.iit

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

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

    Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

    ACS Central Science, vol. 3, (no. 9), pp. 949-960
    Article
  • 2017
    Lapelosa M.iit

    Conformational dynamics and free energy of BHRF1 binding to Bim BH3

    Biophysical Chemistry, vol. 232, pp. 22-28
    Article
  • 2017
    Ferrarotti M. J. , Decherchi S.iit , *Rocchia W.iit

    Distributed Kernel K-Means for Large Scale Clustering

    International Conference on Artificial Intelligence and Soft Computing
    Conference Paper
  • 2017
    Lapelosa M.iit

    Free Energy of Binding and Mechanism of Interaction for the MEEVD-TPR2A Peptide-Protein Complex

    Journal of Chemical Theory and Computation, vol. 13, (no. 9), pp. 4514-4523
    Article
  • 2017
    *Decherchi S.iit , *Rocchia W.iit

    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
    Article
  • 2016
    *Goldoni L.iit , Beringhelli T. , Rocchia W.iit , Realini N.iit , Piomelli D.iit

    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
    Data Paper
  • 2016
    Sana M.E. , Quilliam L.A. , Spitaleri A.iit , Pezzoli L. , Marchetti D. , Lodrini C. , Candiago E. , Lincesso A.R. , Ferrazzi P. , Iascone M.

    A novel HRAS mutation independently contributes to left ventricular hypertrophy in a family with a known MYH7 mutation

    PLoS ONE, vol. 11, (no. 12)
    Article
  • 2016
    *Goldoni L.iit , Beringhelli T. , Rocchia W.iit , Realini N.iit , Piomelli D.iit

    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
    Article
  • 2016
    Genna V.iit , Gaspari R.iit , Dal Peraro M. , *De Vivo M.iit

    Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η

    Nucleic Acids Research, vol. 44, (no. 6), pp. 2827-2836
    Article
  • 2016
    Spiliotopoulos D. , Kastritis P.L. , Melquiond A.S.J. , Bonvin A.M.J.J. , Musco G. , Rocchia W.iit , Spitaleri A.iit

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

    Frontiers in Molecular Biosciences, vol. 3, (no. AUG)
    Article