Evidence map›Paper›PMID 40118074›Full record

ReviewThe journal of physical chemistry letters2025

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.

Lorenzo Casalino, Carlos A Ramos-Guzmán, Rommie E Amaro, Carlos Simmerling, Alessio Lodola, Adrian J Mulholland, Katarzyna Świderek, Vicent Moliner

Abstract readReview
In one paragraph

Review in The journal of physical chemistry letters, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. The pivotal role of β-lactone stereochemistry in the development of SARS-CoV-2 MProtein science : a publication of the Protein Society · 2026
    Article
  2. Article
  3. Article
  4. Insights into the Catalytic Activity of a Metagenome-Derived Urethanase.Journal of the American Chemical Society · 2025
    Article
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

8 authors.

Lorenzo CasalinoDepartment of Molecular Biology, University of California San Diego, La Jolla, California 92093, United States.ORCID 0000-0003-3581-1148
Carlos A Ramos-GuzmánCentre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.ORCID 0000-0002-7701-377X
Rommie E AmaroDepartment of Molecular Biology, University of California San Diego, La Jolla, California 92093, United States.ORCID 0000-0002-9275-9553
Carlos SimmerlingDepartment of Chemistry and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States.ORCID 0000-0002-7252-4730
Alessio LodolaDipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, I 43121 Parma, Italy.ORCID 0000-0002-8675-1002
Adrian J MulhollandCentre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.ORCID 0000-0003-1015-4567
Katarzyna ŚwiderekBiocomp group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain.ORCID 0000-0002-7528-1551
Vicent MolinerBiocomp group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain.ORCID 0000-0002-3665-3391

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (M

Indexed as

Coronavirus 3C ProteasesCOVID-19Molecular Dynamics SimulationSARS-CoV-2Spike Glycoprotein, CoronavirusAntiviral AgentsHumansPandemicsAntiviral AgentsCoronavirus 3C ProteasesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2

Identifiers

PMID40118074
PMCPMC11973918

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.