Zhang, W;
Howell, SC;
Wright, DW;
Heindel, A;
Qiu, X;
Chen, J;
Curtis, JE;
(2017)
Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates.
Journal of Molecular Graphics and Modelling
, 73
pp. 179-190.
10.1016/j.jmgm.2017.02.010.
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Abstract
We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data.
| Type: | Article |
|---|---|
| Title: | Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.jmgm.2017.02.010 |
| Publisher version: | https://doi.org/10.1016/j.jmgm.2017.02.010 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | Monte Carlo, Torsion angle molecular dynamics, Structural biology, Small-angle scattering, SANSSAXS |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10060010 |
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