Professional Education


  • Doctor of Philosophy, University of California Berkeley (2015)
  • Bachelor of Science, University of Illinois Chicago (2008)

All Publications


  • Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 JOURNAL OF PHYSICAL CHEMISTRY B Wang, L., McKiernan, K. A., Gomes, J., Beauchamp, K. A., Head-Gordon, T., Rice, J. E., Swope, W. C., Martinez, T. J., Pande, V. S. 2017; 121 (16): 4023-4039

    Abstract

    The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.

    View details for DOI 10.1021/acs.jpcb.7b02320

    View details for Web of Science ID 000400534200012

    View details for PubMedID 28306259