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List of works by Walter Rocchia

A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven p<i>K</i><sub>a</sub> Predictions in Proteins

scientific article published on 15 July 2022

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

scientific article published on 10 September 2015

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation.

scientific article published on 12 June 2014

A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale.

scientific article

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

scientific article published on 17 February 2016

AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets.

scientific article published in July 2006

Absolute nutrient concentration measurements in cell culture media: (1)H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches

scientific article

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

scientific article published on 03 August 2018

Application of Conformational Clustering in Protein–Ligand Docking

scientific article published on 01 January 2012

Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution ⬇️

scientific article published on December 6, 2012

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

scientific article published on 17 January 2018

Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition.

scientific article published in September 2009

Corrigendum: Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

scientific article published on 6 May 2016

Describing the Conformational Landscape of Small Organic Molecules through Gaussian Mixtures in Dihedral Space.

scientific article published on June 2014

Electroactive carbon nanotube actuators: Soft-lithographic fabrication and electro-chemical modelling

article by Alberto Mazzoldi et al published August 2008 in Materials Science and Engineering C-Biomimetic and Supramolecular Systems

Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking

scientific article published on 15 October 2021

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

scientific article published on 19 January 2018

Finding Principal Paths in Data Space

scientific article published on 25 December 2018

Force Field Parametrization of Metal Ions from Statistical Learning Techniques.

scientific article

GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi.

scientific article

Green fluorescent protein ground states: the influence of a second protonation site near the chromophore

scientific article

Implicit solvent methods for free energy estimation.

scientific article published on 25 August 2014

Import Vector Domain Description: A Kernel Logistic One-Class Learning Algorithm.

scientific article

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

scientific article published in March 2018

Insights into Ligand-Protein Binding from Local Mechanical Response.

scientific article published on 30 August 2011

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

scientific article

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

scientific article

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

scientific article

Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model

scientific article published in January 2006

Molecular mechanics and dynamics: numerical tools to sample the configuration space

scientific article published on January 2014

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

scientific article published on 01 April 2019

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

scientific article published on 10 November 2016

SDPhound, a Mutual Information-Based Method to Investigate Specificity-Determining Positions

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

scientific article published on 20 August 2018

Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

article

Systematic exploitation of multiple receptor conformations for virtual ligand screening

scientific article

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

scientific article

Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case

scientific article published on 10 December 2020

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