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Lab VI: Advanced SASSIE-web

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.


While we test our prototypes, this module will remain in "Beta", and may not always be accessible and/or stable as new features are added and tested. Refer to the SASSIE-web Google Group for support, watch the GitHub page for current developments, and use the feedback mechanism to report bugs and feature requests.


Basic Usage

The purpose of the module is 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


Demonstration

Protein Backbone B-DNA Single-Stranded Nucleic Acid Backbone Isopeptide Bond
HIV-1 Gag Matrix Protein X
Linear strand of B-DNA X

Exercises

The following table links examples using the each type of flexible region currently available. Please work through each of these examples noting the differences between the different move types. The Torsion Angle Monte Carlo documentation contains additional examples, and will be updated as future move sets are added.

Protein Backbone B-DNA Single-Stranded Nucleic Acid Backbone Isopeptide Bond
Nucleosome Core Particle X X
rpoS mRNA X
Diubiquitin 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., In Press (Accepted 23 July 2016)

  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).

Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

  1. 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).

  2. 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).


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