Recent Work
Recent work using Force Field X is focused on:
- first principles prediction of the structure, thermodynamics and solubility of organic crystals.
- new approaches to accelerate thermodynamics from advanced polarizable force fields (i.e. AMOEBA) using sampling from simple fixed charge models.
- structure prediction and protein design using novel optimization algorithms that account for many-body chemical physics (i.e. the hydrophobic effect, polarization, etc.)
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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Fenn, T. D. and M. J. Schnieders, Polarizable Atomic Multipole X-ray Refinement: Weighting Schemes for Macromolecular Diffraction. Acta Crystallographica Section D 2011 67, (11), 957-65.
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