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Riccardo Baron

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Piotr Setny; Riccardo Baron; J Andrew McCammon; Peter Michael Kekenes-Huskey; Joachim Dzubiella
Solvent fluctuations in hydrophobic cavity-ligand binding kinetics.
Riccardo Baron; J Andrew McCammon
Molecular recognition and ligand association.
Riccardo Baron; Piotr Setny; Francesco Paesani
Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition.

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All Publications

2013: Piotr Setny; Riccardo Baron; J Andrew McCammon; Peter Michael Kekenes-Huskey; Joachim Dzubiella
Solvent fluctuations in hydrophobic cavity-ligand binding kinetics.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(4):1197-202.
2013: Riccardo Baron; J Andrew McCammon
Molecular recognition and ligand association.
Annual review of physical chemistry 2013;64():151-75.
2012: Riccardo Baron; Piotr Setny; Francesco Paesani
Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition.
The journal of physical chemistry. B 2012;116(46):13774-80.
2012: Riccardo Baron; Nadeem A Vellore
LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(31):12509-14.
2012: Riccardo Baron; Nadeem A Vellore
LSD1/CoREST reversible opening-closing dynamics: discovery of a nanoscale clamp for chromatin and protein binding.
Biochemistry 2012;51(15):3151-3.
2011: Sara Elizabeth Nichols; Riccardo Baron; Anthony Ivetac; J Andrew McCammon
Predictive power of molecular dynamics receptor structures in virtual screening.
Journal of chemical information and modeling 2011;51(6):1439-46.
2011: Riccardo Baron; Claudia Binda; Marcello Tortorici; J Andrew McCammon; Andrea Mattevi
Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex.
Structure (London, England : 1993) 2011;19(2):212-20.
2010: Riccardo Baron; Piotr Setny; J Andrew McCammon
Water in cavity-ligand recognition.
Journal of the American Chemical Society 2010;132(34):12091-7.
2010: Lovorka Perić-Hassler; Halvor S Hansen; Riccardo Baron; Philippe H Hünenberger
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
Carbohydrate research 2010;345(12):1781-801.
2009: Riccardo Baron; J Andrew McCammon; Andrea Mattevi
The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation.
Current opinion in structural biology 2009;19(6):672-9.
2009: Riccardo Baron; Conor Riley; Pirom Chenprakhon; Kittisak Thotsaporn; Remko T Winter; Andrea Alfieri; Federico Forneris; Willem J H van Berkel; Pimchai Chaiyen; Marco W Fraaije; Andrea Mattevi; J Andrew McCammon
Multiple pathways guide oxygen diffusion into flavoenzyme active sites.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(26):10603-8.
2009: Moritz Winger; Daniel Trzesniak; Riccardo Baron; Wilfred F van Gunsteren
On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models.
Physical chemistry chemical physics : PCCP 2009;11(12):1934-41.
2008: Sergio E Wong; Riccardo Baron; J Andrew McCammon
Hot-spot residues at the E9/Im9 interface help binding via different mechanisms.
Biopolymers 2008;89(11):916-20.
2008: Alemayehu A Gorfe; Riccardo Baron; J Andrew McCammon
Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect.
Biophysical journal 2008;95(7):3269-77.
2008: Rommie E Amaro; Riccardo Baron; J Andrew McCammon
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
Journal of computer-aided molecular design 2008;22(9):693-705.
2008: Jozica Dolenc; Riccardo Baron; John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren
Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.
Chembiochem : a European journal of chemical biology 2008;9(11):1749-56.
2008: Chia-En Chang; William A McLaughlin; Riccardo Baron; Wei Wang; J Andrew McCammon
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(21):7456-61.
2008: Riccardo Baron; J Andrew McCammon
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.
Chemphyschem : a European journal of chemical physics and physical chemistry 2008;9(7):983-8.
2008: Melissa R Landon; Rommie E Amaro; Riccardo Baron; Chi Ho Ngan; David Ozonoff; J Andrew McCammon; Sandor Vajda
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.
Chemical biology & drug design 2008;71(2):106-16.
2007: Riccardo Baron; J Andrew McCammon
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;46(37):10629-42.
2007: Riccardo Baron; Daniel Trzesniak; André H M de Vries; Andreas Elsener; Siewert J Marrink; Wilfred F van Gunsteren
Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.
Chemphyschem : a European journal of chemical physics and physical chemistry 2007;8(3):452-61.
2006: Riccardo Baron; André H M de Vries; Philippe H Hünenberger; Wilfred F van Gunsteren
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations.
The journal of physical chemistry. B 2006;110(31):15602-14.
2006: Wilfred F van Gunsteren; Dirk Bakowies; Riccardo Baron; Indira Chandrasekhar; Markus Christen; Xavier Daura; Peter Gee; Daan P Geerke; Alice Glättli; Philippe H Hünenberger; Mika A Kastenholz; Chris Oostenbrink; Merijn Schenk; Daniel Trzesniak; Nico F A van der Vegt; Haibo B Yu
Biomolecular modeling: Goals, problems, perspectives.
Angewandte Chemie (International ed. in English) 2006;45(25):4064-92.
2006: Riccardo Baron; André H M de Vries; Philippe H Hünenberger; Wilfred F van Gunsteren
Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.
The journal of physical chemistry. B 2006;110(16):8464-73.
2005: Markus Christen; Philippe H Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P Geerke; Tim N Heinz; Mika A Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; Wilfred F van Gunsteren
The GROMOS software for biomolecular simulation: GROMOS05.
Journal of computational chemistry 2005;26(16):1719-51.
2005: Riccardo Baron; Dirk Bakowies; Wilfred F van Gunsteren
Principles of carbopeptoid folding: a molecular dynamics simulation study.
Journal of peptide science : an official publication of the European Peptide Society 2005;11(2):74-84.
2004: Riccardo Baron; Dirk Bakowies; Wilfred F van Gunsteren
Carbopeptoid folding: effects of stereochemistry, chain length, and solvent.
Angewandte Chemie (International ed. in English) 2004;43(31):4055-9.