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Torsion Angle Monte Carlo (BETA)

Performs molecular Monte Carlo simulations on protein, and B-DNA. Move sets for single-stranded nucleic acids, carbohydrates and polymers are in development.

Accessibility

The Torsion Angle Monte Carlo module is accessible from the Beta section of the main menu.

Basic Usage

The purpose of the module is to perform a molecular simulation by sampling torsion angles. Facilities to incorporate new torsion move-sets are available for developers. Currently, backbone protein, double-stranded nucleic acid are working. One can combine multiple move-set sampling in a single molecular simulation.

Notes

Example usage

The following table links several examples using the types of flexible regions indicated. These examples introduce how to provide input for systems of increasing complexity.

Protein Backbone B-DNA Single-Stranded Nucleic Acid Backbone Isopeptide Bond
HIV-1 Gag Matrix Protein X
Full HIV-1 Gag Protein X
Diubiquitin X
rpoS mRNA X
Linear strand of B-DNA X
Nucleosome Core Particle X X
Tetranucleosome X X

Limitations

The program is written so that linear polymers of proteins, single-stranded nucleic acids, and B-DNA are simulated over a specific selection of residues in a single direction.

Reference(s) and Citations

  1. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints, J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text

  2. Monte Carlo Simulation Algorithm for B-DNA, S. C. Howell, X. Qiu, J. E. Curtis, J. Comput. Chem., 37, 2553-2563 (2016). BIBTeX, EndNote, Plain Text

  3. Conformation of the HIV-1 Gag Protein in Solution, S. A. K. Datta, J. E. Curtis, W. Ratcliff, P. K. Clark, R. M. Crist, J. Lebowitz, S. Krueger, A. Rein, J. Mol. Biol. 365, 812-824 (2007). BIBTeX, Endnote, Plain Text

  4. CHARMM: The energy function and its parameterization with an overview of the program, A. D. MacKerel Jr., C. L. Brooks III, L. Nilsson, B. Roux, Y. Won, M. Karplus, The Encyclopedia of Computational Chemistry, John Wiley & Sons: Chichester, 271-277 (1998). BIBTeX, Endnote, Plain Text

  5. Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins, C. A. Castaneda, E. Dixon, O. Walker, A. Chaturvedi, M. A. Nakasone, J. E. Curtis, M. R. Reed, S. Krueger, T. A. Cropp, D. Fushman, Structure, 24, 424-436 (2016). BibTeX, EndNote, Plain Text

  6. Linkage-specific conformational ensembles of non-canonical polyubiquitin chains, C. A. Castaneda, J. E. Curtis, S. Krueger, D. Fushman, Phys. Chem. Chem. Phys., 18, 5771-88 (2016). BibTeX, EndNote, Plain Text

  7. Structural Model of an mRNA in complex with the bacterial chaperone Hfq, Y. Peng, J. E. Curtis, X. Fang, S. Woodson, Proc. Natl. Acad. Sci. USA 111, 17134-17139 (2014). BibTeX, EndNote, Plain Text

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