JMJS -- Publications

Publications & Talks

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)
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).

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models Dzubiella J., J.M.J. Swanson, J.A. McCammon, Phys. Rev. Lett. 96, 087802 (2006).

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).

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).

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).

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).

Computer Simulation of Water in Cytochrome C Oxidase. Xuehe Zheng, Dmitri Medvedev, Jessica Swanson, Alexei Stuchebrukhov, BBA, 1557: 99-107 (2003).

**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

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.