Riccardo Baron

Riccardo Baron

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Riccardo Baron

Riccardo Baron

Publications by authors named "Riccardo Baron"

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53Publications

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PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms.

J Chem Theory Comput 2014 Nov;10(11):5068-80

Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária , Recife, PE 50740-560, Brazil.

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November 2014

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

J Chem Theory Comput 2014 Sep 1;10(9):4104-20. Epub 2014 Aug 1.

Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112-0850, United States.

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September 2014

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

J Mol Graph Model 2014 Mar 25;48:80-6. Epub 2013 Dec 25.

Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA. Electronic address:

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March 2014

Epigenetic molecular recognition: a biomolecular modeling perspective.

ChemMedChem 2014 Mar 12;9(3):484-94. Epub 2014 Feb 12.

Department of Medicinal Chemistry, College of Pharmacy and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 (USA).

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March 2014

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

BMC Biophys 2013 Nov 25;6(1):15. Epub 2013 Nov 25.

Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA.

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November 2013

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

Authors:
Riccardo Baron

Biophys J 2013 Oct;105(7):1545-6

Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah. Electronic address:

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October 2013

Molecular recognition and ligand association.

Annu Rev Phys Chem 2013 5;64:151-75. Epub 2013 Mar 5.

Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820, USA.

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September 2013

Thiuram disulfides as pseudo-irreversible inhibitors of lymphoid tyrosine phosphatase.

ChemMedChem 2013 Sep 19;8(9):1561-8. Epub 2013 Jul 19.

Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.

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September 2013

Substrate selection influences molecular recognition in a screen for lymphoid tyrosine phosphatase inhibitors.

Chembiochem 2013 Sep 16;14(13):1640-7. Epub 2013 Aug 16.

Department of Medicinal Chemistry, University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 (USA).

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September 2013

Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|

J Chem Theory Comput 2013 Sep 1;9(9):4195-4204. Epub 2013 Aug 1.

Department of Mathematics and Center for Theoretical Biological Physics, University of California , San Diego, La Jolla, California 92093-0112, United States.

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September 2013

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics.

Proc Natl Acad Sci U S A 2013 Jan 7;110(4):1197-202. Epub 2013 Jan 7.

Physics Department, Technical University Munich, D-85748 Garching, Germany.

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January 2013

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

J Chem Theory Comput 2013 Jan 26;9(1):46-53. Epub 2012 Oct 26.

Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093-0365, United States ; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California 92093, United States.

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January 2013

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

J Phys Chem B 2012 Nov 7;116(46):13774-80. Epub 2012 Nov 7.

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.

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November 2012

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

J Chem Theory Comput 2012 Oct 14;8(10):3696-704. Epub 2012 Jun 14.

Department of Chemistry and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States.

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October 2012

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

Proc Natl Acad Sci U S A 2012 Jul 16;109(31):12509-14. Epub 2012 Jul 16.

Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT 84112-5820, USA.

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July 2012

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

Methods Mol Biol 2012 ;819:93-103

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA.

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April 2012

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

Methods Mol Biol 2012 ;819:469-86

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA.

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April 2012

LSD1/CoREST reversible opening-closing dynamics: discovery of a nanoscale clamp for chromatin and protein binding.

Biochemistry 2012 Apr 9;51(15):3151-3. Epub 2012 Apr 9.

Department of Medicinal Chemistry, College of Pharmacy, The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States.

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April 2012

Predictive power of molecular dynamics receptor structures in virtual screening.

J Chem Inf Model 2011 Jun 12;51(6):1439-46. Epub 2011 May 12.

Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0365, United States.

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June 2011

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

J Chem Theory Comput 2011 Jun;7(7):2224-2232

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California, U.S.A.

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June 2011

Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex.

Structure 2011 Feb;19(2):212-20

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, and Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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February 2011

Water in cavity-ligand recognition.

J Am Chem Soc 2010 Sep;132(34):12091-7

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California, San Diego, California 92093, USA.

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September 2010

How Can Hydrophobic Association Be Enthalpy Driven?

J Chem Theory Comput 2010 Sep 24;6(9):2866-2871. Epub 2010 Aug 24.

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Pharmacology, University of California, San Diego and Physics Department, Technical University Munich, 85748 Garching, Germany.

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September 2010

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

Carbohydr Res 2010 Aug 1;345(12):1781-801. Epub 2010 Jun 1.

Laboratory of Physical Chemistry, ETH Zürich, ETH Hönggerberg, HCI, CH-8093 Zürich, Switzerland.

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August 2010

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

Curr Opin Struct Biol 2009 Dec 4;19(6):672-9. Epub 2009 Nov 4.

Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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December 2009

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

J Chem Theory Comput 2009 Dec;5(12):3150-3160

Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365 and Laboratory of Physical Chemistry, ETHZ, ETH Hönggerberg, CH 8093, Zürich, Switzerland.

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December 2009

Multiple pathways guide oxygen diffusion into flavoenzyme active sites.

Proc Natl Acad Sci U S A 2009 Jun 16;106(26):10603-8. Epub 2009 Jun 16.

Department of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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June 2009

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

J Chem Theory Comput 2009 Apr 25;5(4):1106-1116. Epub 2009 Mar 25.

Department of Chemistry & Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0365.

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April 2009

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

Phys Chem Chem Phys 2009 Mar 18;11(12):1934-41. Epub 2009 Feb 18.

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zürich, Switzerland.

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March 2009

E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study.

J Phys Chem B 2008 Dec;112(51):16802-14

Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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December 2008

Hot-spot residues at the E9/Im9 interface help binding via different mechanisms.

Biopolymers 2008 Nov;89(11):916-20

Department of Chemistry and Biochemistry, University of California at San Diego, LA Jolla, CA 92093-0365, USA.

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November 2008

Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect.

Biophys J 2008 Oct 11;95(7):3269-77. Epub 2008 Jul 11.

Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093-0365, USA.

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October 2008

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

J Comput Aided Mol Des 2008 Sep 15;22(9):693-705. Epub 2008 Jan 15.

Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365, USA.

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September 2008

Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.

Chembiochem 2008 Jul;9(11):1749-56

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zürich, Switzerland.

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July 2008

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

Chemphyschem 2008 May;9(7):983-8

Department of Chemistry & Biochemistry and Center for Theoretical and Biological Physics, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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May 2008

Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.

Proc Natl Acad Sci U S A 2008 May 21;105(21):7456-61. Epub 2008 May 21.

Departments of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365, USA.

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May 2008

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.

Biochemistry 2007 Sep 24;46(37):10629-42. Epub 2007 Aug 24.

Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, USA.

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September 2007

Configurational entropy elucidates the role of salt-bridge networks in protein thermostability.

Protein Sci 2007 Jul;16(7):1349-59

Biomolecular Research, Structural Biology Paul Scherrer Institut, Villigen, Switzerland.

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July 2007

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

Chemphyschem 2007 Feb;8(3):452-61

Laboratorium für Physikalische Chemie, ETH, Swiss Federal Institute of Technology Zürich, 8093 Zürich, Switzerland.

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February 2007

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

Biophys J 2006 Aug 26;91(4):1460-70. Epub 2006 May 26.

Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.

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August 2006

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations.

J Phys Chem B 2006 Aug;110(31):15602-14

Laboratorium für Physikalische Chemie, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland.

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August 2006

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

Biophys J 2006 Jun 31;90(12):4337-44. Epub 2006 Mar 31.

Laboratory of Physical Chemistry, ETH-Hönggerberg, Zürich, Switzerland.

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June 2006

The GROMOS software for biomolecular simulation: GROMOS05.

J Comput Chem 2005 Dec;26(16):1719-51

Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.

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December 2005

Principles of carbopeptoid folding: a molecular dynamics simulation study.

J Pept Sci 2005 Feb;11(2):74-84

Laboratorium für Physikalische Chemie, ETH, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.

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February 2005

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

Angew Chem Int Ed Engl 2004 Aug;43(31):4055-9

Laboratorium für Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland.

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August 2004