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27.  Perič-Hassler L, Hansen HS, Baron R, Hünenberger PH.
       Conformational properties of glucose-based disaccharides using molecular dynamics simulations with local elevation umbrella sampling.
       In preparation.

26.  Baron R, McCammon JA, Mattevi A.
       The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: Structural biology and biomolecular simulation
       Curr. Opin. Struct. Biol., 2009; 19: 1-8.

25.  Baron R, Hünenberger PH, McCammon JA.
       Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: Correction terms and convergence properties
       J. Chem. Theory Comput., in press.

24.  Baron R, Riley C, Chenprakhon P, Thotsaporn K, Winter RT, Alfieri A, Forneris F, van Berkel WJH, Chaiyen P, Fraaije MW, Mattevi A, McCammon JA.
       Multiple pathways guide oxygen diffusion into flavoenzyme active sites
       Proc. Natl. Acad. Sci. USA, 2009; 106: 10603-10608.   SM
       Nature Chemistry Highlight (Biochemistry & Theoretical chemistry)

23.  Lawrenz M, Baron R, McCammon JA.
       Independent-trajectories thermodynamic-integration free-energy changes for biomolecular systems: Determinants of H5N1 avian influenza neuraminidase inhibition by peramivir
       J. Chem. Theory Comput., 2009; 5: 1106-1116.

22.  Winger M, Trzesniak D, Baron R, van Gunsteren WF.
       On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models
       Phys. Chem. Chem. Phys., 2009; 11: 1934-1941.

21.  Wong SE, Baron R, McCammon JA.
       Hot-spot residues at the E9/Im9 interface help binding via different mechanisms
       Biopolymers, 2008; 89: 916-920.

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
       J. Phys. Chem. B, 2008; 112: 16802-16814.

19.  Gorfe AA, Baron R, McCammon JA.
       Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven hydrophobic effect
       Biophys. J., 2008; 95: 3269-3277.   SM

18.  Dolenč 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, 2008: 9: 1749-1756.   SM

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., 2008; 22: 693-705.

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 molecular dynamics 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.    Dolenč 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.

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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. Dr. 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.

*Denotes equal contributions.

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