Chris Baker

Postdoctoral Fellow
University of Maryland Baltimore
School of Pharmacy

chris "at" outerbanks "dot" umaryland "dot" edu
(410) 706-7441

CV (pdf)

I studied chemistry at the University of Oxford, gaining my first experiences in computational chemistry during an internship at the Medicines Research Centre of GlaxoSmithKline. I then spent the final year of my undergraduate degree working in the group of Prof. Graham Richards and Dr. Guy Grant. I stayed in Oxford with Prof. Richards and Dr. Grant to complete my D.Phil., with a year spent as a visiting student at the Unilever Centre for Molecular Informatics at the University of Cambridge. Following my D.Phil. and a brief period as a visiting researcher in the Protein Mechanics and Evolution Group at the CAS-MPG Partner Institute for Computational Biology in Shanghai, I began my current position as a Postdoctoral Fellow at the University of Maryland Baltimore in September 2008.

Research Interests

Broadly speaking, my interests lie in using computational tools to gain an improved understanding of the fundamental physical forces that determine inter- and intra-molecular interactions; building improved computational tools to provide better representations of those interactions, and using those tools to obtain new insights into biochemical phenomena. At present my work is focussed primarily on the development of the CHARMM Drude polarizable force field, with a specific interest in the development of parameters for the treatment of the nucleic acids. To date, this work has focussed mainly on the optimzation of parameters associated with small molecule analogues of the functional groups present within the nucleic acids (see publications, below). This aspect of the project is largely completed, and I am now moving towards working with more macromolecular data, the ultimate aim being the development of a robust a reliable polarizable force field for the treatment of all DNA and RNA molecules. Within the CHARMM Drude polarizable force field, I'm also interested in the optimization of Lennard-Jones parameter combining rules for the improved representation of solvation.

I also have a second project, in the area of drug design. Working in collaboration with the group of Dr. Jing Chen (Emory University) we are focusing on the computationally-assisted discovery of novel inhibitors of protein-protein interactions involving 14-3-3, a potential drug target for the treatment of human 8p11 myeloproliferative syndrome.

Publications

13. Baker, C. M.; Anisimov, V. M.; MacKerell Jr., A. D. "Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model" J. Chem. Phys. B 2011, 115, 580-596.

12. Baker, C. M.; Lopes, P. E. M.; Zhu, X.; Roux, B.; MacKerell Jr., A. D. “Accurate Calculation of Hydration Free Energies using the CHARMM Drude Polarizable Force Field" J. Chem. Theory Comput. 2010, 6, 1181-1198.

* Cover Article *

11. Baker, C. M.; MacKerell Jr., A. D, “Polarizability Rescaling and atom-based Thole Scaling in the CHARMM Drude Polarizable Force Field for Ethers” J. Mol. Model. 2010, 16, 567-576.

10. Banham, J. E.; Baker, C. M.; Ceola, S.; Day, I. J.; Grant, G. H.; Groenen, E. J. J.; Rodgers, C. T.; Jeschke, G.; Timmel, C. R. “Distance measurements in the borderline region of applicability of CW EPR and DEER: A model study on a homologous series of spin-labelled peptides” J. Mag. Res. 2008, 191, 202-218.

9. Baker, C. M.; Grant, G. H. “The Effect of Solvation on Biomolecular Conformation: 2-Amino-1-phenylethanol” J. Phys. Chem. B 2007, 111, 9940-9954.

8. Baker, C. M.; Grant, G. H. “Role of Aromatic Amino Acids in Protein-Nucleic Acid Recognition” Biopolymers 2007, 85, 456-470.

7. Baker, C. M.; Grant ,G. H. “Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine” J. Chem. Theory Comput. 2007, 3, 530-548.

6. Comméiras, L.; Moses, J. E.; Adlington, R. M.; Baldwin, J. E.; Cowley, A. R.; Baker, C. M.; Albrecht, B.; Grant, G. H. “Total synthesis of the epoxyquinol dimer (+)-panepophenanthrin: application of a diastereospecific biomimetic Diels-Alder dimerisation”  Tetrahedron 2006, 62, 9892-9901.

5. Baker, C. M.; Grant, G. H. “The Structure of Liquid Benzene” J. Chem. Theory Comput. 2006, 2, 947-955.

4. Baker, C. M.; Grant, G. H. “A solvent induced mechanism for conformational change”  Chem. Commun. 2006, 1387-1389.

3. Macleod, N. A.; Butz, P.; Simons, J. P.; Grant, G. H.; Baker, C. M.; Tranter, G. E. “Structure, electronic circular dichroism and Raman optical activity in the gas phase and in solution: a computational and experimental investigation” Phys. Chem. Chem. Phys. 2005, 7, 1432-1440.

2. Claridge, T. D. W.; Long, D. D.; Baker, C. M.; Odell, B.; Grant, G. H.; Edwards, A. A.; Tranter, G. E.; Fleet, G. W. J.; Smith, M. D. “Helix-Forming Carbohydrate Amino Acids”  J. Org. Chem. 2005, 70, 2082-2090.

1. Macleod, N. A.; Butz, P.; Simons, J. P.; Grant, G. H.; Baker, C. M.; Tranter, G. E. “Electronic Circular Dichroism Spectroscopy of 1-(R) Phenylethanol: The “Sector Rule” Revisited and an Exploration of Solvent Effects” Isr. J. Chem. 2004, 44, 27-36.