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57 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

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

Ferrarotti M.J.^iit , *Rocchia W.^iit , Decherchi S.^iit

Finding Principal Paths in Data Space

IEEE Transactions on Neural Networks and Learning Systems

DOI 10.1109/TNNLS.2018.2884792

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

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

Bernetti M. , Masetti M. , *Rocchia W.^iit , Cavalli A.^iit

Kinetics of drug binding and residence time

Annual Review of Physical Chemistry

DOI 10.1146/annurev-physchem-042018-052340

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

DOI 10.1093/bioinformatics/bty761

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

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

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)

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
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

DOI 10.1038/srep25299

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

DOI 10.1021/acs.jmedchem.5b01643

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

DOI 10.1021/acs.jctc.6b00475

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

DOI 10.1016/j.neunet.2015.10.011

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

DOI 10.1021/acs.jcim.5b00169

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

DOI 10.1007/978-3-319-12211-3_10

Book Chapter

57 publications found

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

Finding Principal Paths in Data Space

Force Field Parametrization of Metal Ions from Statistical Learning Techniques

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

Kinetics of drug binding and residence time

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

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

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

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor

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

A Pipeline to Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

Building and Analyzing Molecular Surfaces: A Tutorial on NanoShaper