RNA

Biocomputational methods complement experimental techniques to expand our understanding of RNA, molecules vital to the normal expression of genes within our bodies.

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News

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New package added: MMB 3.14 for Windows

MMB (MacroMoleculeBuilder) Apr 7, 2021
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ForceBalance version 1.7.0 released!

ForceBalance : Systematic Force Field Optimization Dec 3, 2019
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OpenSim gets high marks as a multibody system simulator

Simbody: Multibody Physics API Aug 3, 2015

Publications

P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and V. S. Pande. "OpenMM 7: Rapid development of high performance algorithms for molecular dynamics." PLOS Comp. Biol. 13(7): e1005659.

Tek, A., Korostelev, A.A. and Flores, S.C. (2015) MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory. Nucleic Acids Res., 10.1093/nar/gkv1457.

Wang, L-P., Martinez, T. J. and Pande, V.S. "Building force fields - an automatic, systematic and reproducible approach", submitted.

Discussion

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Re: Reflecting walls and velocity modification

OpenMM Aug 8, 2022
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Re: Out-of-plane bend error

OpenMM Aug 2, 2022
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Re: Can OpenMM run and analyze mixed solvent MD?

OpenMM Jul 27, 2022

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

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