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Selected Recent Publications with Force Field X

CpHMD CSP
Year Publication
2024 Gogal, R., Nessler, A., Thiel, A., Bernabe H., Corrigan Grove, R., Cousineau, L., Litman, J., Miller J., Qi G., Speranza M., Tollefson M., Fenn T., Michaelson, J., Okada, O., Piquemal, JP., Ponder, J., Shen, J., Smith, R., Yang, W., Ren P. and Schnieders M. Force Field X: A Computational Microscope to Study Genetic Variation and Organic Crystals Using Theory and Experiment Journal of Chemical Physics 2024, 161, 012501.
Thiel, A., Speranza, M., Jadhav, S., Stevens, L., Unruh, D., Ren, P., Ponder, J., Shen, J. and Schnieders, M. Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field. Journal of Chemical Theory and Computation 2024, 20(7), 2921-2933.
Nessler, A., Okada, O., Kinoshita, Y., Nishimura, K., Nagata, H., Fukuzawa, K., Yonemochi, E. and Schnieders, M. Crystal Polymorph Search in the NPT Ensemble via a Deposition/Sublimation Alchemical Path. Crystal Growth & Design 2024 24(8), 3205-3217.
2023 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.
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.
2022 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.
2021 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.
2019 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.
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.
2016 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.
Bell, D., Qi, R., Jing, Z., Xiang, J. Y., Mejias, C., Schnieders, M., Ponder, J., and P. Ren, Calculating binding free energies of host-guest systems using AMOEBA polarizable force field. Physical Chemistry Chemical Physics 2016, 18 (44), 30261-30269.
2015 LuCore, S. D., Litman, J. M., Powers, K. T., Gao, S., Lynn, A. M., Tollefson, W. T. A., Fenn, T. D., Washington, M. T. and M. J. Schnieders, Dead-End Elimination with a Polarizable Force Field Repacks PCNA Models. Biophysical Journal 2015, 109 (4), 816-826.
Shi, Y., Schnieders, M. J., Piquemal, J.-P., and P. Ren, Polarizable Force Fields for Biomolecular Modeling. Reviews in Computational Chemistry 2015 Edition: 28, Publisher: Springer, Editors: Kenny B. Lipkowitz
2014 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.