The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
GPU-accelerated molecular modeling coming of age
Open accessAbstract
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely for visualization of molecular structures and animation of trajectories resulting from molecular dynamics simulations. Modern GPUs have evolved into fully programmable, massively parallel co-processors that can now be exploited to accelerate many scientific computations, typically providing about one order of magnitude speedup over CPU code and in special cases providing speedups of two orders of magnitude. This paper surveys the development of molecular modeling algorithms that leverage GPU computing, the advances already made and remaining issues to be resolved, and the continuing evolution of GPU technology that promises to become even more useful to molecular modeling. Hardware acceleration with commodity GPUs is expected to benefit the overall computational biology community by bringing teraflops performance to desktop workstations and in some cases potentially changing what were formerly batch-mode computational jobs into interactive tasks.
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Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Self-citationFast Parallel Algorithms for Short-Range Molecular Dynamics
Plimpton, S. (1995) · Journal of Computational Physics · doi:10.1006/jcph.1995.1039 · Cited by 44,721
Scalable molecular dynamics with NAMD
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Cited by
Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems
Keith, J. A., Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., Müller, K.-R., & Tkatchenko, A. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.1c00107 · Cited by 849
To milliseconds and beyond: challenges in the simulation of protein folding
Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409
Agent-based modelling in synthetic biology
Gorochowski, T. E. (2016) · Essays in Biochemistry · doi:10.1042/ebc20160037 · Cited by 86
Quantum Computing for Molecular Biology**
Baiardi, A., Christandl, M., & Reiher, M. (2023) · ChemBioChem · doi:10.1002/cbic.202300120 · Cited by 93
Suárez, E., Wiewiora, R. P., Wehmeyer, C., Noé, F., Chodera, J. D., & Zuckerman, D. M. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.0c01154 · Cited by 65
Metadata
- Authors
- Stone, J. E., Hardy, D. J., Ufimtsev, I. S., & Schulten, K.
- Venue
- Journal of Molecular Graphics and Modelling
- Publisher
- Elsevier BV
- Published
- 2010-09
- Volume
- 29
- Issue
- 2
- Pages
- 116-125
- ISSN
- 1093-3263 (ISSN-L)
- OpenAlex
- W2065963893
- Cited by
- 411
- References
- 3
- FWCI
- 59.77
- Type
- journal article
- Language
- en
- Open access
- green
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