Evidence map›Paper›PMID 39163795›Full record

ReviewCurrent opinion in structural biology2024

Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.

Karissa Sanbonmatsu

Abstract readReview
In one paragraph

Review in Current opinion in structural biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

1 author.

Karissa SanbonmatsuLos Alamos National Laboratory, United States; New Mexico Consortium, New Mexico. Electronic address: kys@lanl.gov.

Funding

Large-Scale Simulations of Ribosomal DecodingR01GM072686 · NIGMS · UNIVERSITY OF CALIF-LOS ALAMOS NAT LAB · PI SANBONMATSU, KARISSA Y · 2005 to 2024
$5.5M
Structure-based Simulation of Riboswitches: Electrostatic EffectsR01GM110310 · NIGMS · TRIAD NATIONAL SECURITY, LLC · PI SANBONMATSU, KARISSA Y · 2015 to 2023
$2.6M
NIGMS NIH HHS R01 GM072686NIGMS NIH HHS R01 GM110310
6 · The paper itself

Abstract

Molecular simulations of biological systems tend to be significantly more compute-intensive than those in materials science and astrophysics, due to important contributions of long-range electrostatic forces and large numbers of time steps (>1E9) required. Simulations of biomolecular complexes of microseconds to milliseconds are considered state-of-the-art today. However, these time scales are miniscule in comparison to physiological time scales relevant to molecular machine activity, drug action, and elongation cycles for protein synthesis, RNA synthesis, and DNA synthesis (seconds to days). While an exascale supercomputer has simulated an entire virus for nanoseconds, this supercomputer would need to be 10 billion times faster to simulate that virus for 3 hours of physiological time, demonstrating the insatiable need for computing power. With growing interest in computational drug design from the pharmaceutical sector, the biological sciences are positioned to be an industry driver in computing.

Indexed as

Molecular Dynamics SimulationBiological Science Disciplines

Identifiers

PMID39163795
PMCPMC13242954

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.