Anton, a special-purpose machine for molecular dynamics simulation
By David E. Shaw, Martin M. Deneroff, Ron O. Dror, J. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, K. Bowers, Jack C. Chao and 17 more. CACM, 2008
583 citations recorded by the source corpus.
Subfields: Hardware and Architecture, Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/d73a16fc661c380fec35be136a7a84c0cea6cc40
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In Molecular Biology
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- Jianyi Yang
In Spectroscopy
Citations in the corpus
- Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “…have also been designed specifically for MD calculations; for example, a supercomputer named Anton was conceived as a “computational microscope” and was developed with the idea to reach previously inaccessible simulation timescales within a reasonable computation time (Shaw et al., 2008).”
- TPU v4: An Optically Reconfigurable Supercomputer for Machine Learning with Hardware Support for Embeddings (2023, unknown): “Traditional supercomputers also employ tightly connected multiprocessors over 3D tori with a high-bandwidth interconnect [15, 50].”
- Toward the solution of the protein structure prediction problem (2021, background): “Since then, technology has progressed through the use of more advanced computer architectures (122, 123) and force fi elds (124 – 130), but molecular dynamics-based structure prediction still remains impractical for proteins of typical length.”
- Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design (2013, methodology): “The timescales often simulated with MD using today’s computers are nanoseconds to microseconds and sometimes even milliseconds (36).”
- Variational Encoding of Complex Dynamics (2017, unknown): “This can be done by considering the mean squared error between the predicted propagation, x′ t+τ , and the true propagation, xt+τ , along with the Kullback–Leibler divergence between latent space priors that generate x′ t+τ : Lreconstruction = ∥∥x′ t+τ − xt+τ∥∥+ 1+ logσ2−μ2−σ2 2 , (2)”