Riccardo Baron

发表

On the use of molecular dynamics receptor conformations for virtual screening.

J Andrew McCammon, Sara E Nichols, Riccardo Baron, 2012, Methods in molecular biology.

The GROMOS software for biomolecular simulation: GROMOS05

Markus Christen, Chris Oostenbrink, Wilfred F. van Gunsteren, 2005, J. Comput. Chem..

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

Victor H Rusu, Roberto D Lins, Riccardo Baron, 2014, Journal of molecular graphics & modelling.

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

Rommie E. Amaro, James Andrew McCammon, Riccardo Baron, 2008, J. Comput. Aided Mol. Des..

Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin

Riccardo Baron, Andrea Mattevi, Nadeem A. Vellore, 2013, PLoS Comput. Biol..

Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

James Andrew McCammon, Riccardo Baron, Sara E. Nichols, 2011, J. Chem. Inf. Model..

Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing.

Yi Wang, J Andrew McCammon, Riccardo Baron, 2012, Methods in molecular biology.

Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble

David Ozonoff, Sandor Vajda, Rommie E Amaro, 2008, Chemical biology & drug design.

(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.

J Andrew McCammon, Riccardo Baron, J. Mccammon, 2008, ChemPhysChem.

Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.

Wilfred F van Gunsteren, Riccardo Baron, Martin Müller, 2006, Biophysical journal.

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

J. Andrew McCammon, Morgan Lawrenz, Riccardo Baron, 2009, Journal of chemical theory and computation.

Hydrophobic Association and Volume‐Confined Water Molecules

J. Andrew McCammon, Piotr Setny, Riccardo Baron, 2012 .

Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies.

Yi Wang, J Andrew McCammon, Morgan Lawrenz, 2011, Journal of chemical theory and computation.

Computational Drug Discovery and Design

Riccardo Baron, R. Baron, 2012, Methods in Molecular Biology.

On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations

César Augusto F. de Oliveira, J. Andrew McCammon, Riccardo Baron, 2012, Journal of chemical theory and computation.

Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties

J. Andrew McCammon, Riccardo Baron, Philippe H. Hünenberger, 2009, Journal of chemical theory and computation.

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.

Wilfred F van Gunsteren, Riccardo Baron, Philippe H Hünenberger, 2006, The journal of physical chemistry. B.

Fast sampling of A-to-B protein global conformational transitions: from Galileo Galilei to Monte Carlo anisotropic network modeling.

Riccardo Baron, R. Baron, 2013, Biophysical journal.

Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition

Riccardo Baron, R. Baron, N. Vellore, 2013, BMC biophysics.

Carbopeptoid folding: effects of stereochemistry, chain length, and solvent.

Wilfred F van Gunsteren, Riccardo Baron, Dirk Bakowies, 2004, Angewandte Chemie.

Biomolecular modeling: Goals, problems, perspectives.

Wilfred F van Gunsteren, Chris Oostenbrink, Xavier Daura, 2006, Angewandte Chemie.

E9-Im9 Colicin DNase−Immunity Protein Biomolecular Association in Water: A Multiple-Copy and Accelerated Molecular Dynamics Simulation Study

J. Andrew McCammon, Riccardo Baron, Sergio E. Wong, 2008, The journal of physical chemistry. B.

How Can Hydrophobic Association Be Enthalpy Driven?

J. Andrew McCammon, Piotr Setny, Riccardo Baron, 2010, Journal of chemical theory and computation.

Multiple pathways guide oxygen diffusion into flavoenzyme active sites

J Andrew McCammon, Conor Riley, Riccardo Baron, 2009, Proceedings of the National Academy of Sciences.

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding.

Wilfred F van Gunsteren, Chris Oostenbrink, Joze Koller, 2006, Biophysical journal.

Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations.

J Andrew McCammon, Riccardo Baron, J. Mccammon, 2007, Biochemistry.

Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition.

Piotr Setny, Riccardo Baron, Francesco Paesani, 2012, The journal of physical chemistry. B.

LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition

Riccardo Baron, R. Baron, N. Vellore, 2012, Proceedings of the National Academy of Sciences.

β-Peptides with Different Secondary-Structure Preferences: How Different Are Their Conformational Spaces?

Xavier Daura, Riccardo Baron, Wilfred F. van Gunsteren, 2002 .

Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.

Riccardo Baron, Halvor S. Hansen, Philippe H Hünenberger, 2010, Carbohydrate research.

Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations.

Valeria Molinero, Riccardo Baron, R. Baron, 2012, Journal of chemical theory and computation.

On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.

Wilfred F van Gunsteren, Riccardo Baron, Daniel Trzesniak, 2009, Physical chemistry chemical physics : PCCP.

Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Wilfred F van Gunsteren, Siewert J Marrink, Riccardo Baron, 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization.

Yuqing Qiu, Valeria Molinero, Riccardo Baron, 2014, Journal of chemical theory and computation.

The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation.

J Andrew McCammon, Riccardo Baron, Andrea Mattevi, 2009, Current opinion in structural biology.

Principles of carbopeptoid folding: a molecular dynamics simulation study

Wilfred F van Gunsteren, Riccardo Baron, Dirk Bakowies, 2005, Journal of peptide science : an official publication of the European Peptide Society.