Result: Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.
Title:
Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.
Authors:
Gogal RA; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Nessler AJ; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Thiel AC; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Bernabe HV; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Corrigan Grove RA; Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA., Cousineau LM; Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA., Litman JM; Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA., Miller JM; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Qi G; Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA., Speranza MJ; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Tollefson MR; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Fenn TD; Analytical Development, LEXEO Therapeutics, New York, New York 10010, USA., Michaelson JJ; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA., Okada O; Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan., Piquemal JP; Department of Chemistry, Sorbonne Université, F-75005 Paris, France., Ponder JW; Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA., Shen J; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA., Smith RJH; Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA., Yang W; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA., Ren P; Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA., Schnieders MJ; Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA.; Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA.
Source:
The Journal of chemical physics [J Chem Phys] 2024 Jul 07; Vol. 161 (1).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: American Institute of Physics Country of Publication: United States NLM ID: 0375360 Publication Model: Print Cited Medium: Internet ISSN: 1089-7690 (Electronic) Linking ISSN: 00219606 NLM ISO Abbreviation: J Chem Phys Subsets: MEDLINE
Imprint Name(s):
Publication: New York, NY : American Institute of Physics
Original Publication: Lancaster, Pa., American Institute of Physics.
Original Publication: Lancaster, Pa., American Institute of Physics.
MeSH Terms:
References:
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Proteins. 2006 Nov 15;65(3):712-25. (PMID: 16981200)
Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):957-65. (PMID: 22101822)
Clin Obstet Gynecol. 2020 Mar;63(1):109-119. (PMID: 31876640)
J Comput Chem. 2022 Sep 5;43(23):1530-1542. (PMID: 35778723)
BMC Ophthalmol. 2020 Oct 1;20(1):388. (PMID: 33004036)
J Chem Phys. 2008 Sep 28;129(12):124105. (PMID: 19045004)
J Comput Chem. 2002 Nov 15;23(14):1297-304. (PMID: 12214312)
Biophys J. 2005 Jul;89(1):141-57. (PMID: 15863480)
J Chem Theory Comput. 2014 Sep 9;10(9):3626-33. (PMID: 26588507)
J Chem Theory Comput. 2012 Mar 13;8(3):810-23. (PMID: 26593343)
J Chem Theory Comput. 2014 Jul 8;10(7):2781-91. (PMID: 26586507)
Proteins. 2004 Sep 1;56(4):738-52. (PMID: 15281127)
Int J Mol Sci. 2021 Oct 18;22(20):. (PMID: 34681887)
J Chem Phys. 2004 Jan 1;120(1):73-87. (PMID: 15267263)
Cryst Growth Des. 2024 Mar 09;24(8):3205-3217. (PMID: 38659664)
Phys Chem Chem Phys. 2016 Nov 9;18(44):30313-30322. (PMID: 27524378)
J Comput Chem. 2017 Apr 15;38(10):740-752. (PMID: 28160511)
Science. 1983 Aug 19;221(4612):709-13. (PMID: 6879170)
J Chem Theory Comput. 2014 Feb 28;10(4):1638-1651. (PMID: 26512230)
J Chem Theory Comput. 2024 Apr 9;20(7):2921-2933. (PMID: 38507252)
J Chem Phys. 2023 Aug 7;159(5):. (PMID: 37526158)
J Chem Theory Comput. 2011 Aug 9;7(8):2617-29. (PMID: 26606635)
J Chem Theory Comput. 2013;9(9):4046-4063. (PMID: 24163642)
J Dent Res. 2017 Oct;96(11):1339-1345. (PMID: 28825856)
J Mol Biol. 1987 Feb 20;193(4):775-91. (PMID: 2441069)
Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):1024-31. (PMID: 20823553)
Eye (Lond). 2018 Apr;32(4):843-845. (PMID: 29350691)
Proteins. 2004 May 1;55(2):383-94. (PMID: 15048829)
Nat Protoc. 2007;2(11):2728-33. (PMID: 18007608)
J Comput Aided Mol Des. 2022 Apr;36(4):263-277. (PMID: 35597880)
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2016 Aug 1;72(Pt 4):439-59. (PMID: 27484368)
JAMA Ophthalmol. 2023 Sep 1;141(9):872-879. (PMID: 37589989)
J Comput Chem. 2004 Aug;25(11):1400-15. (PMID: 15185334)
Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):952-65. (PMID: 19690373)
J Chem Phys. 2014 May 14;140(18):184101. (PMID: 24832247)
J Am Chem Soc. 2010 Jun 2;132(21):7252-3. (PMID: 20446682)
Curr Eye Res. 2020 Jan;45(1):91-96. (PMID: 31361967)
Sci Rep. 2022 Jul 11;12(1):11743. (PMID: 35817949)
Science. 1983 May 13;220(4598):671-80. (PMID: 17813860)
J Chem Theory Comput. 2011 Apr 12;7(4):1141-56. (PMID: 26606362)
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. (PMID: 9757107)
J Appl Crystallogr. 2022 Nov 21;55(Pt 6):1528-1537. (PMID: 36570662)
Biophys J. 1994 May;66(5):1335-40. (PMID: 8061189)
J Chem Theory Comput. 2018 Oct 9;14(10):5273-5289. (PMID: 30176213)
Nature. 1992 Apr 9;356(6369):539-42. (PMID: 21488406)
J Chem Theory Comput. 2010 Aug 10;6(8):2253-66. (PMID: 26613484)
J Chem Theory Comput. 2011 Oct 11;7(10):3143-3161. (PMID: 22022236)
Proteins. 2000 Aug 15;40(3):389-408. (PMID: 10861930)
J Phys Chem B. 2024 Jan 11;128(1):109-116. (PMID: 38154096)
Chem Sci. 2017 Nov 27;9(4):956-972. (PMID: 29732110)
Curr Pharm Des. 2006;12(17):2111-20. (PMID: 16796559)
Hum Genet. 2023 Jun;142(6):819-834. (PMID: 37086329)
Mol Vis. 2017 Mar 30;23:179-184. (PMID: 28400699)
J Phys Chem B. 1998 Apr 30;102(18):3586-616. (PMID: 24889800)
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20227-32. (PMID: 19075242)
Biophys J. 2019 Aug 6;117(3):602-612. (PMID: 31327459)
J Chem Theory Comput. 2007 Jan 1;3(1):156-169. (PMID: 21072141)
J Chem Theory Comput. 2012 May 8;8(5):1721-1736. (PMID: 22582032)
Nature. 2021 Aug;596(7873):583-589. (PMID: 34265844)
J Chem Theory Comput. 2021 Apr 13;17(4):2323-2341. (PMID: 33769814)
J Chem Theory Comput. 2019 Aug 13;15(8):4602-4614. (PMID: 31268700)
J Phys Chem B. 2010 Mar 4;114(8):2549-64. (PMID: 20136072)
Am J Hum Genet. 2018 Oct 4;103(4):484-497. (PMID: 30245029)
PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. (PMID: 30735498)
J Chem Phys. 2009 Feb 21;130(7):074101. (PMID: 19239278)
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2016 Apr;72(Pt 2):171-9. (PMID: 27048719)
Hum Mol Genet. 2016 Jan 1;25(1):44-56. (PMID: 26494905)
PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. (PMID: 28746339)
Biophys J. 2015 Aug 18;109(4):816-26. (PMID: 26287633)
J Chem Theory Comput. 2018 Apr 10;14(4):2084-2108. (PMID: 29438622)
Methods Mol Biol. 2007;350:205-23. (PMID: 16957325)
J Comput Chem. 2017 Sep 5;38(23):2047-2055. (PMID: 28600826)
J Chem Theory Comput. 2007 Nov;3(6):2083-97. (PMID: 26636202)
J Am Soc Nephrol. 2016 Apr;27(4):1245-53. (PMID: 26283675)
Proteins. 2006 Nov 15;65(3):712-25. (PMID: 16981200)
Acta Crystallogr D Biol Crystallogr. 2011 Nov;67(Pt 11):957-65. (PMID: 22101822)
Clin Obstet Gynecol. 2020 Mar;63(1):109-119. (PMID: 31876640)
J Comput Chem. 2022 Sep 5;43(23):1530-1542. (PMID: 35778723)
BMC Ophthalmol. 2020 Oct 1;20(1):388. (PMID: 33004036)
J Chem Phys. 2008 Sep 28;129(12):124105. (PMID: 19045004)
J Comput Chem. 2002 Nov 15;23(14):1297-304. (PMID: 12214312)
Biophys J. 2005 Jul;89(1):141-57. (PMID: 15863480)
J Chem Theory Comput. 2014 Sep 9;10(9):3626-33. (PMID: 26588507)
J Chem Theory Comput. 2012 Mar 13;8(3):810-23. (PMID: 26593343)
J Chem Theory Comput. 2014 Jul 8;10(7):2781-91. (PMID: 26586507)
Proteins. 2004 Sep 1;56(4):738-52. (PMID: 15281127)
Int J Mol Sci. 2021 Oct 18;22(20):. (PMID: 34681887)
J Chem Phys. 2004 Jan 1;120(1):73-87. (PMID: 15267263)
Cryst Growth Des. 2024 Mar 09;24(8):3205-3217. (PMID: 38659664)
Phys Chem Chem Phys. 2016 Nov 9;18(44):30313-30322. (PMID: 27524378)
J Comput Chem. 2017 Apr 15;38(10):740-752. (PMID: 28160511)
Science. 1983 Aug 19;221(4612):709-13. (PMID: 6879170)
J Chem Theory Comput. 2014 Feb 28;10(4):1638-1651. (PMID: 26512230)
Grant Information:
R35 GM148261 United States GM NIGMS NIH HHS; R01 GM106137 United States GM NIGMS NIH HHS; R01 DC012049 United States DC NIDCD NIH HHS; R01 GM124621 United States GM NIGMS NIH HHS; R01 GM114237 United States GM NIGMS NIH HHS
Substance Nomenclature:
0 (Proteins)
0 (Nucleic Acids)
0 (Nucleic Acids)
Entry Date(s):
Date Created: 20240703 Date Completed: 20240703 Latest Revision: 20250829
Update Code:
20250829
PubMed Central ID:
PMC11223778
DOI:
10.1063/5.0214652
PMID:
38958156
Database:
MEDLINE
Further Information
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.
(© 2024 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND) license (https://creativecommons.org/licenses/by-nc-nd/4.0/).)