scientific
publications
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21.
Wong SE, Baron R, McCammon JA.
Cooperativity explains hot-spot
residues' binding thermodynamics: Case study of the Glu41 hot-spot at
the E9 Dnase/Im9 interface.
In preparation.
20. Baron R, Wong SE, de
Oliveira CAF, McCammon JA.
E9-Im9 colicin Dnase-Immunity
protein biomolecular association in water: A
multiple-copy and accelerated MD simulation study.
In preparation.
19. Gorfe AA, Baron R,
McCammon JA.
Water-membrane partition
thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven
hydrophobic effect.
Biophys.
J., in press.
18.
Dolenc J, Baron R, Missimer
JH, Steinmetz
MO, van
Gunsteren WF.
Exploring the conserved water sites and
hydration of a coiled-coil trimerization motif: A MD simulation study.
ChemBioChem,
in press.
17.
Chang CEA, McLaughlin WA, Baron
R, Wang W, McCammon JA.
Entropic
contributions and the
influence of the hydrophobic environment in promiscuous protein-protein
association
Proc.
Natl. Acad. Sci. USA, 2008; 105: 7456-7461.
16.
Baron R, McCammon JA.
(Thermo)dynamic
role of receptor
flexibility, entropy, and motional correlation in protein-ligand
binding
ChemPhysChem,
2008; 9: 983-988.
15.
Amaro RE, Baron R, McCammon JA.
An
improved relaxed complex scheme for
receptor flexibility in computer-aided drug design
J.
Comput. Aid. Mol. Des., in press.
14.
Landon MR, Amaro RE, Baron R,
Ngan CH, Ozonoff D, McCammon JA, Vadja S.
Novel
druggable hot spots in avian
influenza neuraminidase H5N1 revealed by computational solvent mapping
of a reduced and representative receptor ensemble
Chem.
Biol. Drug. Des., 2008; 71: 106-116.
13.
Baron R, McCammon JA.
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: 10629-10642. SM
12.
Missimer
JH, Steinmetz MO, Baron R,
Winkler FK, Kammerer RA,
Daura X, van Gunsteren WF.
Configurational entropy elucidates the role of
salt-bridge networks in protein thermostability
Protein
Sci. 2007; 16: 1349-1359. SM
11.
Baron R, Trzesniak D, de Vries AH, Elsener
A,
Marrink SJ, van Gunsteren WF.
Comparison
of thermodynamic properties of coarse-grained and atomic-level
simulation models
ChemPhysChem 2007; 8: 452-461.
SM
10. Baron R, de
Vries AH, Hünenberger PH, van Gunsteren WF.
Configurational
entropies of lipids in pure and mixed bilayers from atomic-level and
coarse-grained simulations
J. Phys. Chem. B
2006; 110: 15602-15614.
SM
9. Baron
R, van Gunsteren WF,
Hünenberger PH.
Estimating
the configurational entropy
from
molecular dynamics simulations: anharmonicity and correlation
corrections
to the quasi-harmonic approximation
Trends in Physical Chemistry, 2006;
11: 87-122.
8.
Dolenc J, Baron R,
Oostenbrink
C,
Koller J, van Gunsteren WF.
Configurational
entropy change of netropsin and distamycin upon DNA minor-groove binding
Biophys. J. 2006; 91:
1460-1470.
7.
van Gunsteren WF, Bakowies D, Baron R,
Chandrasekhar I, Christen
M,
Daura X, Gee PJ, Geerke DP,
Glättli A, Hünenberger PH,
Kastenholz
MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB.
Biomolecular
modeling: goals, problems, perspectives
Angew. Chem. Int. Ed. 2006; 45:
4064-4092.
6.
Pereira CS, Kony D, Baron
R,
Müller M, van
Gunsteren WF, Hünenberger PH.
Conformational and
dynamical properties of disaccharides in water: a molecular dynamics
study
Biophys. J. 2006; 90:
4337-4344. ERR
5. Baron R,
de Vries AH,
Hünenberger
PH, van Gunsteren WF.
Comparison of atomic-level and coarse-grained
models for liquid hydrocarbons from molecular dynamics configurational
entropy estimates
J. Phys. Chem. B
2006; 110: 8464-8473. SM
4. Christen M, Hünenberger PH,
Bakowies D, Baron R,
Bürgi R, Geerke DP,
Heinz
TN, Kastenholz MA,
Kräutler V, Oostenbrink C, Peter
C,
Trzesniak D, van Gunsteren WF.
The GROMOS
software for biomolecular simulation: GROMOS05
J. Comput. Chem. 2005; 26:
1719-1751.
3. Baron
R, Bakowies D, van Gunsteren WF.
Principles of
carbopeptoid folding: a molecular dynamics simulation study
J. Peptide Sci. 2005; 11:
74-84.
2. Baron R, Bakowies D, van Gunsteren
WF.
Carbopeptoid
Folding: Effects of Stereochemistry, Chain Length, and Solvent
Angew. Chem. Int. Ed. 2004; 43: 4055-4059. SM
1. Baron R, Bakowies D, van Gunsteren
WF, Daura X.
Peptides with
different secondary-structure preferences: how different are their
conformational spaces?
Helv.
Chim. Acta 2002;
85: 3872-3882.
0. Baron R.
Biomolecular simulation: calculation of
entropy and free energy, polypeptide and carbopeptoid folding,
simplification of the force field for
lipid simulations.
Doctoral
thesis ETH 16584, Swiss
Federal Institute of Technology Zurich
Accepted on recommendation of Prof. Dr.
Wilfred F van Gunsteren (examiner) and
Prof. Dr. Ulrich W Suter, Dr. Philippe
H Hünenberger, Dr. Dirk Bakowies (co-examiners).
-1. Baron R.
Studi cristallografici sulla fenolo
idrossilasi
da Bacillus thermoglucosidasius mediante
diffrazione di raggi x.
Laurea thesis, matricola 550209,
Università
degli Studi di Milano (IT), October 2001.
Accepted under the supervision of Prof.
Andrea
Mattevi and Prof. Riccardo Destro.
-2. Baron R.
Expression, Purification and Folding
studies
of FRB.
Research project report, Chemistry
Laboratory,
University of Cambridge (UK), June 2000.
Project supervisors: Dr. Sophie
Jackson
and Dr. Farid Khan.
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