Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimizat...

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Bibliographic Details
Published in:The Journal of chemical physics Vol. 161; no. 1
Main Authors: Gogal, Rose A, Nessler, Aaron J, Thiel, Andrew C, Bernabe, Hernan V, Corrigan Grove, Rae A, Cousineau, Leah M, Litman, Jacob M, Miller, Jacob M, Qi, Guowei, Speranza, Matthew J, Tollefson, Mallory R, Fenn, Timothy D, Michaelson, Jacob J, Okada, Okimasa, Piquemal, Jean-Philip, Ponder, Jay W, Shen, Jana, Smith, Richard J H, Yang, Wei, Ren, Pengyu, Schnieders, Michael J
Format: Journal Article
Language:English
Published: United States 07-07-2024
Subjects:
Algorithms
Crystallization
Genetic Variation
Molecular Dynamics Simulation
Nucleic Acids - chemistry
Proteins - chemistry
Software
Thermodynamics
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Description
Summary:Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
ISSN:1089-7690
DOI:10.1063/5.0214652