2. Publications

72 publications found

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  • 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
    DOI 10.1016/j.mri.2020.01.006
    Article in Press
  • 2020
    Bendandi A. , Dante S.iit , Zia S. R. , Diaspro A.iit , *Rocchia W.iit

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

    Frontiers in Molecular Biosciences
    DOI 10.3389/fmolb.2020.00015
    Article in Press
  • 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
    DOI 10.1039/c9cc06182g
    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)
    DOI 10.1002/adhm.201901182
    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
    DOI 10.1007/s12559-019-09651-1
    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
    DOI 10.1109/TNNLS.2018.2884792
    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
    DOI 10.1146/annurev-physchem-042018-052340
    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
    DOI 10.1002/9783527806836.ch2
    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
    DOI 10.1093/bioinformatics/bty761
    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
    DOI 10.1007/s00249-019-01373-4
    Conference Paper
  • 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
    DOI 10.1021/acs.jcim.7b00680
    Article
  • 2018
    Lapelosa M.iit

    Conformational dynamics and free energy of BHRF1 binding to Bim BH3

    Biophysical Chemistry, vol. 232, pp. 22-28
    DOI 10.1016/j.bpc.2017.11.001
    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)
    DOI 10.1021/acs.jcim.8b00489
    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
    DOI 10.1021/acs.jctc.7b01088
    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
    DOI 10.1021/acs.jctc.7b00779
    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)
    DOI 10.1063/1.5019596
    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
    DOI 10.3390/mol2net-04-06101
    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
    DOI 10.1002/open.201800121
    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
    DOI 10.1021/acscentsci.7b00211
    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
    DOI 10.5121/csit.2017.71015
    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
    DOI 10.1021/acs.jctc.7b00105
    Article