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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

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

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. , 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

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

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

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-04-06143

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

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
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
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

DOI 10.1109/TNNLS.2016.2547220

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

DOI 10.1016/j.dib.2016.05.054

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)

DOI 10.1371/journal.pone.0168501

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

DOI 10.1016/j.ab.2016.02.009

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

DOI 10.1093/nar/gkw128

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)

DOI 10.3389/fmolb.2016.00046

Article

64 publications found

Cognitive Insights into Sentic Spaces Using Principal Paths

Finding Principal Paths in Data Space

Kinetics of Drug Binding and Residence Time

Mesoscale bottom-up approach to the study of chromatin compaction: from single nucleosome to chromatin fibre

Mesoscale bottom-up approach to the study of chromatin compaction: from single nucleosome to chromatin fibre

Molecular Dynamics-based approaches describing protein binding

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

PypKa: A flexible Poisson-Boltzmann-based python API for pKa calculations

BiKi Life Sciences: A New Suite for Molecular Dynamics and Related Methods in Drug Discovery

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))

Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach

Force Field Parametrization of Metal Ions from Statistical Learning Techniques

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

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

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

Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis

Conformational dynamics and free energy of BHRF1 binding to Bim BH3

Distributed Kernel K-Means for Large Scale Clustering

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

Import vector domain description: A kernel logistic one-class learning algorithm

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

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

A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using quantitative nuclear magnetic resonance

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

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