naotohori / sop-gpu

Software package for simulations of biomolecules on GPU.

SOP-GPU

The SOP-GPU package, where SOP-GPU stands for the Self Orginized Polymer Model fully implemented on a Graphics Processing Unit (GPU), is a scientific software package designed to perform Langevin Dynamics simulations of the mechanical unfolding/deformation of large biomolecular systems on the experimental subsecond (millisecond-to-second) timescale. The SOP-GPU package utilizes the Cα-atom based coarse-grained description of proteins combined with Langevin Dynamics in overdamped limit.

The package is fully-implemented on GPU using NVIDIA CUDA technology with focus on high-performance, ease of use, and extensibility [1,2]. SOP-GPU provides out-of-the-box capabilities for numerical simulations of nanoindentation experiments, as well as force-ramp and force-clamp protein pulling. One of the features is optinal support for inclusion of hydrodynamics interactions [3].

SOP-GPU have been successfully used to model such system as Fibrin(ogen) molecules [4], CCMV capsid [5,6], microtubule protofilament [7,8,9], human synaptotagmin 1 [10], and muscle anchoring complex [11].

Documentation

Latest documentation is available at ReadTheDocs (PDF).

Licensing

This software is distributed under GPLv3 or later (see COPYING).

If used for scientific publications, please cite [1] and [2]. If hydrodyamics functionality is used, please also cite [3].

Citations

1. Zhmurov, A., Dima, R. I., Kholodov, Y., & Barsegov, V. SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors. Proteins 78, 2984–99 (2010)
2. Zhmurov, A., Rybnikov, K., Kholodov, Y., & Barsegov, V. Generation of random numbers on graphics processors: forced indentation in silico of the bacteriophage HK97. J. Phys. Chem. B 115, 5278–88 (2011)
3. Alekseenko, A., Kononova, O., Kholodov, Y., Marx, K.A., & Barsegov, V. SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies. J. Comput. Chem., in press (2016)
4. Zhmurov, A., Brown, A.E.X., Litvinov, R.I., Dima, R.I., Weisel, J.W., & Barsegov, V. Mechanism of fibrin(ogen) forced unfolding. Structure 19, 1615–24 (2011)
5. Kononova, O., Snijder, J., Brasch, M., Cornelissen, J., Dima, R.I., Marx, K.A., Wuite, G.J.L., Roos, W.H., & Barsegov, V. Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico. Biophys. J. 105, 1893–903 (2013)
6. Kononova, O., Snijder, J., Kholodov, Y., Marx, K.A., Wuite, G.J.L., Roos, W.H., & Barsegov, V. Fluctuating nonlinear spring model of mechanical deformation of biological particles. PLOS Comput. Biol. 12, e1004729 (2016)
7. Kononova, O., Kholodov, Y, Theisen, K.E., Marx, K.A., Dima, R.I., Ataullakhanov, F.I., Grishchuk, E.L., & Barsegov, V. Tubulin bond energies and microtubule biomechanics determined from nanoindentation in silico. J. Am. Chem. Soc. 136(49), 17036–45 (2014)
8. Theisen, K.E., Zhmurov, A., Newberry, M.E., Barsegov, V., & Dima, R.I. Multiscale modeling of the nanomechanics of microtubule protofilaments. J. Phys. Chem. B 116(29), 8545–8555 (2012).
9. Theisen, K.E., Desai, N.J., Volski, A.M., & Dima, R.I. Mechanics of severing for large microtubule complexes revealed by coarse-grained simulations. J. Chem. Phys. 139(12), 121926 (2013).
10. Duan, L., Zhmurov, A., Barsegov, V., & Dima, R.I. Exploring the mechanical stability of the C2 domains in human synaptotagmin 1. J. Phys. Chem. B 115(33), 10133–10146 (2011).
11. Bodmer, N.K., Theisen, K.E., & Dima, R.I. Molecular investigations into the mechanics of a muscle anchoring complex. Biophys. J 108(9), 2322–2332 (2015).