Force Field X – Methods

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Method Development

Novel methods being developed within Force Field X include:

Implicit Solvents	Development of generalized Kirkwood implicit solvents for the polarizable AMOEBA force field.
Crystal Structure Prediction	A complete alchemical pipeline to predict of the structure, stability and solubility of organic crystals.
Advanced Free Energy Methods	Efficient free energy methods for advanced force fields using orthogonal space tempering and dual-topology methods.
Protein Missense Variants	Protein structure optimization using novel many-body expansion algorithms in the context of understanding deafness genetics.
Next Generation Structure Refinement	Advanced methods for refinement of structures against experimental data.

Implicit Solvent Models based on the Generalized Kirkwood Model

Corrigan, R. A., Thiel, A. C., Lynn, J. R., Casavant, T. L., Ren, P., Ponder, J. W., and Schnieders, M. J., A Generalized Kirkwood Implicit Solvent for the Polarizable AMOEBA Protein Model. Journal of Chemical Physics 2023, 159, 054102.
Corrigan, R. A., Qi, G., Thiel, A. C., Lynn, J. R., Walker, B. D., Casavant, T. L., Lagardere, L., Piquemal, J.-P., Ponder, J. W., Ren, P., and Schnieders, M. J., Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation 2021, 17 (4), 2323-2341.

Understanding Protein Missense Variants in the Context of Deafness Genetics

Tollefson, M. R., Gogal, R. A., Weaver, A. M., Schaefer, A. M., Marini, R. J., Azaiez, H., Kolbe, D. L., Wang, D., Weaver, A. E., Casavant, T. L., Braun, T. A., Smith, R. J. H., and Schnieders, M. J., Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome. Human Genetics 2023, 142, 819–834.
Tollefson, M. R., Litman, J. M., Qi, G., O’Connell, C. E., Wipfler, M. J., Marini, R. J., Bernabe, H. V., Tollefson, W. T. A., Braun, T. A., Casavant, T. L., Smith, R. J. H. and M. J. Schnieders, Structural Insights into Hearing Loss Genetics from Polarizable Protein Repacking. Biophysical Journal 2019, 117 (3), 602-612.

Prediction of the Structure, Stability and Solubility of Organic Crystals

Nessler, A. J., Okada, O., Hermon, M. J., Nagata, H., and Schnieders, M. J., Progressive Alignment of Crystals: Reproducible and Efficient Assessment of Crystal Structure Similarity. Journal of Applied Crystallography 2022, 55, 1528-1537.
Dybeck, E. C., Thiel, A., Schnieders, M. J., Pickard, F. C. I. V., Wood, G. P. F., Krzyzaniak, J. F., and Hancock, B. C., A Comparison of Methods for Computing Relative Anhydrous–Hydrate Stability with Molecular Simulation, Crystal Growth and Design 2022, 23, 142-167.
Park, J., Nessler, I., McClain, B., Macikenas D., Baltrusaitis, J. and M. J. Schnieders, Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy. Journal of Chemical Theory and Computation 2014 10, (7), 2781-2791.

Alchemical Free Energy Methods for Advanced Force Fields

Litman, J. M., Thiel, A. C., and M. J. Schnieders, Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding. Journal of Chemical Theory and Computation 2019, 15 (8), 4602-4614.
Nessler, I. J., Litman, J. M., and M. J. Schnieders, Toward Polarizable AMOEBA Thermodynamics at Fixed Charge Efficiency Using a Dual Force Field Approach. Physical Chemistry Chemical Physics 2016, 18 (44), 30313-30322.
Schnieders, M. J., J. Baltrusaitis, Y. Shi, G. Chattree, L. Zheng, W. Yang and P. Ren The Structure, Thermodynamics, and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. Journal of Chemical Theory and Computation 2012 8, (5), 1721–36.