Publications & Talks
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Journal Articles
- Testing the limits of end-point free energy calculations with FKBP12 Swanson J.M.J., J. A. McCammon, (in preparation).
- Optimizing Poisson dielectric boundaries: Lessons learned with atom-centered dielectric functions Swanson J.M.J., J. A. McCammon, (in preparation)
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Coupling nonpolar and polar solvation free energies in implicit solvent models Dzubiella J., J.M.J. Swanson, J.A. McCammon, J. Chem. Phys. 124, 084905 (2006).
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Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models Dzubiella J., J.M.J. Swanson, J.A. McCammon, Phys. Rev. Lett. 96, 087802 (2006).
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The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2 Minh, D.D.L., J.M. Bui, C.E. Chang, T. Jain, J.M.J. Swanson, J.A. McCammon, Biophys. J. 89, L25-L27 (2005).
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Limitations of Atom-Centered Dielectric Functions in Implicit Solvent ModelsSwanson, J.M.J., J. Mongan, and J.A. McCammon, J. Phys. Chem. B, 109, 31, 14769-14772 (2005).
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Optimized radii for Poisson-Boltzmann calculations with the AMBER force field Swanson, J.M.J., S.A. Adcock, and J.A. McCammon, J. Chem. Theory Comput. (3); 484-493 (2005).
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Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy Swanson, J.M.J., R.H. Henchman, J.A. McCammon. Biophys. J., 86, 67-74 (2004).
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Computer Simulation of Water in Cytochrome C Oxidase. Xuehe Zheng, Dmitri Medvedev, Jessica Swanson, Alexei Stuchebrukhov, BBA, 1557: 99-107 (2003).
Talks (** indicates invited talk)
- **UC Davis, Department of Chemistry Seminar Series - Davis, CA October 25, 2005
Protein-ligand interactions: Insights from computer simulations
- **Telluride Science Research Center - Protein Dynamics, Telluride, CO August 1-5, 2005
Insights into protein-protein and protein-ligand association from end-point free energy calculations
- 229TH ACS National Meeting - Comp Division, San Diego, CA, March 13-17, 2005
End-point free energy calculations: What it takes for success with FK506 Binding Protein
- 49th Biophysical Society Meeting, Long Beach, CA, February 12-16, 2005
End-point free energy calculations of FK506BP: Piecing together an energetic puzzle.
- **228th ACS National Meeting - Comp Division, Philadelphia, PA, August 22-26, 2004
End-point free energy calculations: Synergy from continuum solvent and molecular dynamics methods
- **La Jolla Computational Theory Symposium, San Diego, CA. July 31, 2004
Synergy between implicit and explicit solvent models: Optimized radii for Poisson Boltzmann calculations
- 227th ACS National Meeting - Comp Division, Anaheim, CA. March 25 - April 1 2004
Revisiting free energy calculations: One step closer to rigorous scoring functions and one step beyond MM/PBSA
Conference Posters
- 49th Annual Biophysical Society Meeting, Long Beach, CA, February 12-16, 2005
Bridging microscopic and macroscopic models: Using explicit solvent density and charge distribution functions to optimize continuum calculations
- Computational Chemistry Gordon Research Conference, Plymouth, NH July 4 - 9 2004
Optimizing Poisson Boltzmann Continuum Solvent Calculations. Swanson J.M.J., S. Adcock, J.A. McCammon
- Chemical Computing Group Excellence Award for the 227th ACS National Meeting
End-point Free Energy Calculations: Moving beyond MM/PBSA
- Multiscale Computational Modeling for Biomedical Research, San Diego, CA March 25-27, 2004
Connecting Microscopic and Macroscopic Realms: Optimized Radii for Continuum Solvent Calculations
- 47th Annual Biophysical Society Meeting, San Antonio, TX March 1-5, 2003
Applying the statistical mechanics behind ligand-receptor binding affinities.
- 45th Annual Biophysical Society Meeting, Boston, MA Feb 17-21, 2001
Proton pumping channels in cytochrome c oxidase: A structure explored.