scientific publications                        back

56.  Vellore NA, Baron R.
       LSD1/CoREST-H3-Histone Molecular Recognition: Inter-Domain Motions in an Allosteric Clamp Revealed by Computer Simulations
       Biophys. J., 2015; in press.

55.  Lee HK, Zhang L, Smith MD, Walewska A, Vellore NA, Baron R, McIntosh JM, White HS, Olivera BM, Bulaj G.
       A Marine Analgesic Peptide, Contulakin-G, and Neurotensin are Distinct Agonists for Neurotensin Receptors: Uncovering Structural Determinants of Desensitization Properties
       Front. Pharmacol., 2015; 6: 11.

54.  Eiring AM, Page BDG, Kraft IL, Mason CC, Vellore NA, Resetca D, Zabriskie MS, Zhang T, Khorashad J, Engar A, Reynolds KR, Anderson D, Senina AV,
       Pomicter AD, Arpin C, Ahmad S, Heaton W, Tantravahi S, Todic A, Moriggl R, Wolson D, Baron R, O'Hare T, Gunning P, Deininger M.
       Combined STAT3 and BCR-ABL1 Inhibition Induces Synthetic Lethality in Therapy-Resistant Chronic Myeloid Leukemia
       Leukemia, 2015; 29: 586-597.

53.  Lu J, Qiu Y, Baron R, Molinero V.
       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; 10: 4104-4120.

52.  Rusu V, Baron R, Lins RD.
       PITOMBA: Paramater Interface for Oligosaccharide Molecules Based on Atoms
       J. Chem. Theory Comput., 2014; 10: 5068-5080.

51.  Zabriskie MS, Eide CA, Tantravahi SK, Vellore NA, Estrada J, Nicolini FE, Khoury HJ, Larson RA, Konopleva M, Cortes JE, Kantarjian H, Jabbour EJ,
       Kornblau SM, Lipton JH, Rea D, Stenke L, Barbany G, Lange T, Hernandez-Boluda JC, Ossenkoppele GJ, Press RD, Chuah C, Goldberg SL, Wetzler M,
       Mahon FX, Etienne G, Baccarani M, Soverini S, Rosti G, Rousselot P, Friedman R, Deininger M, Reynolds KR, Heaton WL, Eiring AM, Pomicter AD,
       Khorashad JS, Kelley TW, Baron R, Druker BJ, Deininger MW, O'Hare T.
       BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia
       Cancer Cell, 2014; 26: 428-442.

50.  Vellore NA, Baron R.
       Epigenetic Molecular Recognition: A Biomolecular Modeling Perspective
       ChemMedChem, 2014; 9: 484-494.

49.  Rusu VH*, Horta VAC*, Horta BAC, Lins RD, Baron R.
       MDWiZ: A Platform for the Automated Translation of Molecular Dynamics Simulations
       J. Mol. Graph. Model., 2014; 48: 80-86.

48.  Vellore NA, Baron R.
       Molecular Dynamics Simulations Indicate an Induced-Fit Mechanism for LSD1/CoREST-H3-Histone Molecular Recognition
       BMC Biophys., 2013; 6: 15.

47.  Baron R.
       Fast Sampling of A-to-B Protein Global Conformational Transitions: From Galileo Galilei to Monte Carlo Anisotropic Network Modeling
       Biophys J., 2013; 105: 1545-1546.

46.  Zhou S, Rogers KE, de Oliveira CAF, Baron R, Cheng LT, J Dzubiella, B Li, McCammon JA.
       Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril
       J. Chem. Theory Comput., 2013; 9: 4195-4204.

45.  Kulkarni RA, Vellore NA, Bliss MR, Stanford SM, Bottini N, Baron R, Barrios AM.
       Substrate Selection Influences Molecular Recognition in a Screen for Lymphoid Tyrosine Phosphatase Inhibitors
       ChemBioChem, 2013; 14: 1640-1647.

44.  Kulkarni RA, Stanford SM, Vellore NA, Bliss MR, Krishnamurthy D, Baron R, Bottini N, Barrios AM.
       Thiuram Disulfides as Pseudo-irreversible Inhibitors of the Lymphoid Tyrosine Phosphatase
       ChemMedChem, 2013; 8: 1561-1568.

43.  Robertson JC, Hurley N, Tortorici M, Ciossani G, Borrello MT, Vellore NA, Ganesan A, Mattevi A, Baron R.
       Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin
       PLoS Comput. Biol., 2013; 9: e1003158.

42.  Tortorici M, Borrello T, Tardugno M, Chiarelli L, Pilotto S, Ciossani G, Vellore NA, Bailey S, Cowan J, O'Connell M, Crabb SJ, Packham G, Mai A, Baron R, Ganesan A, Mattevi A.
       Protein Recognition by Small Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase
       ACS Chem. Biol., 2013; 8: 1677-1682.

41.  Setny P, Baron R, Kekenes-Huskey PM, McCammon JA, Dzubiella J.
       Solvent Fluctuations in Hydrophobic Cavity-Ligand Binding Kinetics
       Proc. Natl. Acad. Sci. USA, 2013; 110: 1197-1202.

40.  Baron R, McCammon JA.
       Molecular Recognition and Ligand Association
       Ann. Rev. Phys. Chem., 2013; 64: 151-175.

39.  Rogers KE, Ortiz-Sanchez JM, Baron R, Fajer M, de Oliveira CAF, McCammon JA.
       On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations
       J. Chem. Theory Comput., 2013; 9: 46-53.

38.  Baron R, Setny P, Paesani F.
       Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity-Ligand Recognition
       J. Phys. Chem. B, 2012; 46: 13774-13780.

37.  Setny P*, Baron R*, McCammon JA.
       Comment on "Molecular Driving Forces of the Pocket-Ligand Hydrophobic Association" by G. Graziano, Chem. Phys. Lett. 533 (2012) 95
       Chem. Phys. Lett., 2012; 555: 306-309.

36.  Baron R, Molinero V.
       Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations
       J. Chem. Theory Comput., 2012; 7: 3696-3704.

35.  Baron R, Vellore NA.
       LSD1/CoREST is an Allosteric Nanoscale Clamp Regulated by H3-Histone-Tail Molecular Recognition
       Proc. Natl. Acad. Sci. USA, 2012; 109: 12509-12514.

34.  Baron R, Vellore NA.
       LSD1/CoREST Reversible Opening/Closing Dynamics: Discovery of a Nanoscale Clamp for Chromatin and Protein Binding
       Biochemistry, 2012; 51: 3151-3153.

33.  Baron R, Setny P, McCammon JA.
       Hydrophobic Association and Volume-Confined Water Molecules
       In Methods & Principles in Med. Chem. - Protein-Ligand Interactions, 2012; Gohlke H (Ed.), Wiley-VCH.

32.  Lawrenz M, Baron R, Wang Y, McCammon JA.
       Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies
       J. Chem. Theory Comput., 2011; 7: 2224-2232.

31.  Nichols SE, Baron R, Ivetac AD, McCammon JA.
       Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening
       J. Chem. Inf. Model., 2011; 51: 1439-1446.

30.  Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A.
       Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase LSD1-CoREST Complex
       Structure, 2011; 19: 212-220.
       San Diego Supercomputer Center Press Release

29.  Baron R*, Setny P*, McCammon JA.
       Water in cavity-ligand recognition
       J. Am. Chem. Soc., 2010; 132: 12091-12097.
       Nature Chemistry Highlight (Physical Chemistry & Theoretical chemistry)

28.  Setny P*, Baron R*, McCammon JA.
       How can hydrophobic association be enthalpy-driven?
       J. Chem. Theory Comput., 2010: 6: 2866-2871.
       Nature Chemistry Highlight (Physical Chemistry & Theoretical chemistry)
       Cited by Faculty of 1000

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
       Carbohydr. Res., 2010; 345: 1781-1801.

26.  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., 2009; 5: 3150-3160.

25.  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: 672-679.

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.    Lawrenz M, Baron R, Wang Y, McCammon JA.
       Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing
       Methods Mol. Biol. 2012; 819: 469-486.

-1.   Nichols SE, Baron R, McCammon JA.
       On The Use of Molecular Dynamics Receptor Conformations for Virtual Screening
       Methods Mol. Biol. 2012; 819: 93-103.

-2.   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).

-3.   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.

-4.   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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