90 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
    Siryk S. , Bendandi A. , Diaspro A. , *Rocchia W.iit

    Charged dielectric spheres interacting in electrolytic solution: a linearized Poisson-Boltzmann equation model

    Journal of Chemical Physics
    Article in Press
  • 2021
    Adedeji Olulana A.F. , Soler M.A.iit , Lotteri M. , Vondracek H. , Casalis L. , Marasco D. , Castronovo M. , Fortuna S.

    Computational evolution of beta-2-microglubulin binding peptides for nanopatterned surface sensors

    International Journal of Molecular Sciences, vol. 22, (no. 2), pp. 1-18
    Article
  • 2021
    *Soler M.A.iit , Medagli B. , Wang J. , Oloketuyi S. , Bajc G. , Huang H. , Fortuna S. , De Marco A.

    Effect of humanizing mutations on the stability of the llama single-domain variable region

    Biomolecules, vol. 11, (no. 2), pp. 1-14
    Article
  • 2021
    Riccardi L.iit , Decherchi S.iit , Rocchia W.iit , Zanoni G. , Cavalli A.iit , Mancin F. , *De Vivo M.iit

    Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint

    Journal of Physical Chemistry Letters, vol. 12, (no. 23), pp. 5616-5622
    Article
  • 2021
    Bhati A.P. , Wan S. , Alfè D. , Clyde A. R. , Bode M. , Tan L. , Titov M. , Merzky A. , Turilli M. , Jha S. , Highfield R. R. , Rocchia W.iit , Scafuri N. , Succi S. , Kranzlmüller D. , Mathias G. , Wifling D. , Donon Y. , Di Meglio A. , Vallecorsa S. , Ma H. , Trifan A. , Ramanathan A. , Brettin T. , Partin A. , Xia F. , Duan X. , Stevens R. , Coveney P. V.

    Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers

    Interface Focus
    Article in Press
  • 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
    Le Gratiet A.iit , Lanzano L.iit , Bendandi A.iit , Marongiu R.iit , Bianchini P.iit , Sheppard C.iit , Diaspro A.iit

    Phasor approach of Mueller matrix optical scanning microscopy for biological tissue imaging

    Biophysical Journal, vol. 120, (no. 15), pp. 3112-3125
    Article
  • 2021
    Raffo A. , Fugacci U. , Biasotti S. , *Rocchia W.iit , Liu Y. , Otu E. , Zwiggelaar R. , Hunter D. , Zacharaki E.I. , Psatha E. , Laskos D. , Arvanitis G. , Moustakas K. , Aderinwale T. , Christoffer C. , Shin W.-H. , Kihara D. , Giachetti A. , Nguyen H.-N. , Nguyen T.-D. , Nguyen-Truong V.-T. , Le-Thanh D. , Nguyen H.-D. , Tran M.-T.

    SHREC 2021 Track: Retrieval and classification of protein surfaces equipped with physical and chemical properties

    Computers and Graphics, vol. 99, pp. 1-21
    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, vol. 12, (no. 1), 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
    Salpietro V. , Dixon C.L. , Guo H. , Bello O.D. , Vandrovcova J. , Efthymiou S. , Maroofian R. , Heimer G. , Burglen L. , Valence S. , Torti E. , Hacke M. , Rankin J. , Tariq H. , Colin E. , Procaccio V. , Striano P. , Mankad K. , Lieb A. , Chen S. , Pisani L. , Bettencourt C. , Mannikko R. , Manole A. , Brusco A. , Grosso E. , Ferrero G.B. , Armstrong-Moron J. , Gueden S. , Bar-Yosef O. , Tzadok M. , Monaghan K.G. , Santiago-Sim T. , Person R.E. , Cho M.T. , Willaert R. , Yoo Y. , Chae J.-H. , Quan Y. , Wu H. , Wang T. , Bernier R.A. , Xia K. , Blesson A. , Jain M. , Motazacker M.M. , Jaeger B. , Schneider A.L. , Boysen K. , Muir A.M. , Myers C.T. , Gavrilova R.H. , Gunderson L. , Schultz-Rogers L. , Klee E.W. , Dyment D. , Osmond M. , Parellada M. , Llorente C. , Gonzalez-Penas J. , Carracedo A. , Van Haeringen A. , Ruivenkamp C. , Nava C. , Heron D. , Nardello R. , Iacomino M. , Minetti C. , Skabar A. , Fabretto A. , Hanna M.G. , Bugiardini E. , Hostettler I. , O'Callaghan B. , Khan A. , Cortese A. , O'Connor E. , Yau W.Y. , Bourinaris T. , Kaiyrzhanov R. , Chelban V. , Madej M. , Diana M.C. , Vari M.S. , Pedemonte M. , Bruno C. , Balagura G. , Scala M. , Fiorillo C. , Nobili L. , Malintan N.T. , Zanetti M.N. , Krishnakumar S.S. , Lignani G. , Jepson J.E.C. , Broda P. , Baldassari S. , Rossi P. , Fruscione F. , Madia F. , Traverso M. , De-Marco P. , Perez-Duenas B. , Munell F. , Kriouile Y. , El-Khorassani M. , Karashova B. , Avdjieva D. , Kathom H. , Tincheva R. , Van-Maldergem L. , Nachbauer W. , Boesch S. , Gagliano A. , Amadori E. , Goraya J.S. , Sultan T. , Kirmani S. , Ibrahim S. , Jan F. , Mine J. , Banu S. , Veggiotti P. , Zuccotti G.V. , Ferrari M.D. , Van Den Maagdenberg A.M.J. , Verrotti A. , Marseglia G.L. , Savasta S. , Soler M.A.iit , Scuderi C. , Borgione E. , Chimenz R. , Gitto E. , Dipasquale V. , Sallemi A. , Fusco M. , Cuppari C. , Cutrupi M.C. , Ruggieri M. , Cama A. , Capra V. , Mencacci N.E. , Boles R. , Gupta N. , Kabra M. , Papacostas S. , Zamba-Papanicolaou E. , Dardiotis E. , Maqbool S. , Rana N. , Atawneh O. , Lim S.Y. , Shaikh F. , Koutsis G. , Breza M. , Coviello D.A. , Dauvilliers Y.A. , AlKhawaja I. , AlKhawaja M. , Al-Mutairi F. , Stojkovic T. , Ferrucci V. , Zollo M. , Alkuraya F.S. , Kinali M. , Sherifa H. , Benrhouma H. , Turki I.B.Y. , Tazir M. , Obeid M. , Bakhtadze S. , Saadi N.W. , Zaki M.S. , Triki C.C. , Benfenati F.iit , Gustincich S.iit , Kara M. , Belcastro V. , Specchio N. , Capovilla G. , Karimiani E.G. , Salih A.M. , Okubadejo N.U. , Ojo O.O. , Oshinaike O.O. , Oguntunde O. , Wahab K. , Bello A.H. , Abubakar S. , Obiabo Y. , Nwazor E. , Ekenze O. , Williams U. , Iyagba A. , Taiwo L. , Komolafe M. , Senkevich K. , Shashkin C. , Zharkynbekova N. , Koneyev K. , Manizha G. , Isrofilov M. , Guliyeva U. , Salayev K. , Khachatryan S. , Rossi S. , Silvestri G. , Haridy N. , Ramenghi L.A. , Xiromerisiou G. , David E. , Aguennouz M. , Fidani L. , Spanaki C. , Tucci A. , Raspall-Chaure M. , Chez M. , Tsai A. , Fassi E. , Shinawi M. , Constantino J.N. , De Zorzi R. , Fortuna S. , Kok F. , Keren B. , Bonneau D. , Choi M. , Benzeev B. , Zara F. , Mefford H.C. , Scheffer I.E. , Clayton-Smith J. , Macaya A. , Rothman J.E. , Eichler E.E. , Kullmann D.M. , Houlden H.

    AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders

    Nature Communications, vol. 10, (no. 1)
    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