Lista de obras - Walter Rocchia - Dominio Público Uruguay

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

artículo científico publicado en 2022

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

artículo científico publicado en 2015

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Application of Conformational Clustering in Protein–Ligand Docking

artículo científico publicado en 2012

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

artículo científico publicado en 2018

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

artículo científico publicado en 2009

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

artículo científico publicado en 2016

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

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2018

Finding Principal Paths in Data Space

scientific article published on 25 December 2018

Force Field Parametrization of Metal Ions from Statistical Learning Techniques.

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2007

Implicit solvent methods for free energy estimation.

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

Insights into Ligand-Protein Binding from Local Mechanical Response.

artículo científico

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

artículo científico publicado en 2004

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 2006

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

artículo científico publicado en 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.

artículo científico publicado en 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 ⬇️

artículo científico publicado en 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

artículo científico publicado en 2011

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

artículo científico publicado en 2015

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

scientific article published on 10 December 2020

Lista de obras de Walter Rocchia

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

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

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

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

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

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

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

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

Application of Conformational Clustering in Protein–Ligand Docking

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

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

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

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

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

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

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.

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

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

Implicit solvent methods for free energy estimation.

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

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

Insights into Ligand-Protein Binding from Local Mechanical Response.

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

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

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

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

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

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

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

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 ⬇️

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

Systematic exploitation of multiple receptor conformations for virtual ligand screening

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

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