56 publications found

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  • 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
    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
    Ferrarotti M. , *Rocchia W.iit , Decherchi S.

    Finding Principal Paths in Data Space

    IEEE Transactions on Neural Networks and Learning Systems
    Article in Press
  • 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
    Bernetti M. , Masetti M. , *Rocchia W.iit , Cavalli A.

    Kinetics of drug binding and residence time

    Annual Review of Physical Chemistry
    Article in Press
  • 2018
    Decherchi S.iit , Spitaleri A. , Stone J. , *Rocchia W.iit

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

    Bioinformatics
    Article
  • 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
    *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
    Article
  • 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
  • 2016
    Mollica L. , Decherchi S.iit , Zia S.R. , Gaspari R. , Cavalli A.iit , *Rocchia W.iit

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

    Scientific Reports, vol. 6
    Erratum
  • 2016
    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

    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
    Article
  • 2016
    Zia S.R.iit , Gaspari R.iit , Decherchi S.iit , *Rocchia W.iit

    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
    Article
  • 2016
    *Gastaldo P. , *Bisio F. , Decherchi S.iit , *Zunino R.

    SIM-ELM: Connecting the ELM model with similarity-function learning

    Neural Networks, vol. 74, pp. 22-34
    Article
  • 2015
    Spyrakis F. , Benedetti P. , Decherchi S.iit , Rocchia W.iit , Cavalli A.iit , Alcaro S. , Ortuso F. , Baroni M. , Cruciani G.

    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
    Article
  • 2015
    Decherchi S.iit , Rocchia W.iit

    Building and Analyzing Molecular Surfaces: A Tutorial on NanoShaper

    Computational Electrostatics for Biological Applications, Publisher: Springer International Publishing
    Book Chapter
  • 2015
    De Trizio L.iit , Gaspari R.iit , Bertoni G.iit , Kriegel I.iit , Moretti L.iit , Scotognella F.iit , Maserati L.iit , Zhang Y.iit , Messina G.C.iit , Prato M.iit , Marras S.iit , Cavalli A.iit , *Manna L.iit

    Cu3- xP nanocrystals as a material platform for near-infrared plasmonics and cation exchange reactions

    Chemistry of Materials, vol. 27, (no. 3), pp. 1120-1128
    Article
  • 2015
    Decherchi S.iit , Masetti M. , Vyalov I.iit , *Rocchia W.iit

    Implicit solvent methods for free energy estimation

    European Journal of Medicinal Chemistry, vol. 91, pp. 27-42
    Review