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Computational Research in Molecular Chemistry
McCammon Lab News

Undergraduate Research Opportunities

UCSD is the center of an exciting new field of science: computational biology. At the intersection of biochemistry, physics, mathematics, and computing, the field of computational biology uses theoretical and computational models to show how cellular activity emerges from molecular behavior. Research in this field deepens our understanding of biology and is poised to yield dramatic advances in medicine and technology.

The McCammon group invites bright, dedicated undergraduates to join us in shaping this new field. A background that includes multivariate calculus, physical chemistry, and some familiarity with computing is ideal, but all applicants will be considered.

Undergraduate participants may be eligible for an hourly salary and/or academic credit.

Previous undergraduates have become co-authors of journal articles, and have found their work to be very helpful in gaining acceptance at leading graduate and medical schools. Recent examples include:

Work by Erik Hom (subsequently, Ph.D. program in Biophysics, UCSF):

  • Helms, V., E.F.Y. Hom, T.P. Straatsma, J.A. McCammon, P. Langhoff. Exciting Green Fluorescent Protein, in "Combined Quantum Mechanical and Molecular Mechanical Methods," J. Gao, M.A. Thompson, Eds., ACS Symposium Series 712, American Chemical Society, Washington, DC, pp. 288-295 (1998).

Work by Paul de Bakker (subsequently, Ph.D. program in Biochemistry, Cambridge University):

  • de Bakker, P.I.W., P.H. Hunenberger, J.A. McCammon. Molecular Dynamics Simulations of the Hyperthermophilic Protein Sac7d from Sulfolobus acidocaldarius: Contribution of Salt Bridges to Thermostability. J. Mol. Biol. 285, 1811-1830 (1999).

Work by Kevin Masukawa (subsequently, Ph.D. program in Pharmaceutical Chemistry, UCSF):

  • Carlson, H.A., K.M. Masukawa, J.A. McCammon. Method for Including the Dynamic Fluctuations of a Protein in Computer-aided Drug Design. J. Phys. Chem. A 103, 10213-10219 (1999).
  • Carlson, H.A., K.M. Masukawa, K. Rubins, F.D. Bushman, W.L. Jorgensen, R.D. Lins, J.M. Briggs, J.A. McCammon. Developing a Dynamic Pharmacophore Model for HIV-1 Integrase. J. Med. Chem. 43, 2100-2114 (2000).

Work by Greg Gidofalvi (subsequently, Ph.D. program in Chemistry, University of Chicago):

  • Gidofalvi, G., C.F. Wong, J.A. McCammon. Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A. J. Chem. Educ.,79, 1122-1126 (2002).

Work by Christine Gould (subsequently, Ph.D. program in Biomedical Sciences, UCSD):

  • Gould, G., C.F. Wong. Designing Specific Protein Kinase Inhibitors: Insights from Computer Simulations and Comparative Sequence/Structure Analysis. Pharmacology and Therapeutics, 93, 169-178 (2002).

Work by Chiansan Ma (subsequently, Ph.D. program in Chemistry, M.I.T.):

  • Ma, C., N.A. Baker, S. Joseph, J.A. McCammon. Binding of Aminoglycoside Antibiotics to the Small Ribosomal Subunit: a Continuum Electrostatics Investigation, J. Amer. Chem. Soc., 124, 1438-1442(2002).

Work by Angelique Eslami ( subsequently, Ph.D program in Biosciences, University of Iowa):

  • Kua, J., Y. Zhang, A.C. Eslami, J.R. Butler, J.A. McCammon. Studying the Roles of W86, E202, Y337 in Binding Acetylcholine to Acetylcholinesterase using a Combined Molecular Dynamics and Multiple Docking Approach, Protein Science 12, 2675-2684 (2003).

Work by Peter Sims (subsequently, Ph.D. program in Chemistry, Harvard University):

  • Sims, P.A., C.F. Wong, J.A. McCammon. A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 Inhibitors, J. Med. Chem., 26, 3314-3325 (2003).
  • Sims, P.A. C.F. Wong, J.A. McCammon. Charge Optimization of the Interface between Protein Kinases and their Ligands. J. Comp. Chem. 25,1416-1429 (2004).
  • Sims, P.A., C.F. Wong, D. Vuga, J.A. McCammon, B.M. Sefton. Relative Contributions of Desolvation, Inter- and Intramolecular Interactions to Binding Affinity in Protein Kinase Systems. J. Comp Chem. 26, 668-681 (2005).

Work by Man-Un "Peter" Ung (subsequently, Ph.D. program in Medicinal Chemistry, Univ. of Michigan at Ann Arbor):

  • Ung, M.U., B. Lu, J.A. McCammon. E230Q Mutation of the Catalytic Subunit of cAMP-dependent Protein Kinase
    Affects Local Structure and the Binding of Peptide Inhibitor. Biopolymers 81, 428-439 (2006).

Work by Lily Cheng (subsequently, in Medical School):

  • Cheng, L.S., R.E. Amaro, D. Xu, W.W. Li, P.W. Arzberger, J.A. McCammon. Ensemble-based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase. J. Med. Chem. 51, 3878-3894 (2008).

Work by Yang Xie (subsequently, Ph.D. program, Georgia Institute of Technology):

  • Cheng, L.T., Y. Xie, J. Dzubiella, J.A. McCammon, J. Che, B. Li.  Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules.  J. Chem. Theory Comput. 5, 257-266 (2009).

Work by Jeffrey Sung (subsequently, graduate program in chemistry, UCSD)

  • Sung, J.C., A.W. Van Wynsberghe, R.E. Amaro, W. W. Li, J.A. McCammon.  The role of secondary sialic acid binding sites in influenza N1 neuraminidase. J. Amer. Chem. Soc. 132, 2883-2885 (2010).

Work by Michelle Zhou (subsequently, M.D. program at UC Irvine)

  • Zhou, M., C. de Oliveira, B. Grant, J.A. McCammon.  Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. PLoS Comp. Biol. 7, article e1002178 (2011).

Work by Kalli Kappel (subsequently, Ph.D. program at Stanford)

  • Kappel, K., J. Wereszczynski, R.T. Clubb, J.A. McCammon.  The Binding Mechanism, Multiple Binding Modes, and Allosteric Regulation of Staphylococcus aureus SrtA Probed by Molecular Dynamics Simulations. Protein Sci. 21, 1858-1871 (2012).
  • Kappel, K., Y. Miao, J.A. McCammon. Accelerated Molecular Dynamics Simulations of Ligand Binding to a Muscarinic G-protein Coupled Receptor. Q. Revs. Biophys. 48, 479-487 (2015).

Work by Rachel Kretsch (subsequently, Ph.D. program at Stanford University )

  • Mermelstein, D.J., C. Lin, G. Nelson, R. Kretsch, J.A. McCammon, R.C. Walker.  Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package. J. Comp. Chem. in press (2018). DOI: 10.1002/jcc.25187

Work by Aishu Venkatramani (subsequently, Ph.D. program at Stanford)

  • Venkatramani, A., C.G. Ricci, E. Oldfield, J.A. McCammon. Remarkable similarity in P. falciparum and P. vivax Geranylgeranyl Diphosphate Synthase (GGPPS) dynamics and its implication for anti-malarial drug design. Chem. Biol. Drug Disc. in press (2018). DOI: 10.1111/cbdd.13170



Please submit the information requested below with copy of your transcript to:

Patti Craft
Fax:  858-534-4974
Hand delivery: 4238 Urey Hall
Campus mail:  M/C 0365

Email Address
School and Major
Expected Date of Graduation
Computing Experience
Brief statement of Specific research interest (50-100 words).
Brief statement of Career plans (50-100 words).



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