Evidence map›Paper›PMID 38594926›Full record

ReviewAnnual review of biochemistry2024

The Art and Science of Molecular Docking.

Joseph M Paggi, Ayush Pandit, Ron O Dror

Abstract readReview
In one paragraph

Review in Annual review of biochemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 184 papers.

0numbers the graph read from it
0cells of the map it votes in
184citing 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

184 citing papers in PubMed.

  1. Article
  2. α-Mangostin attenuatesVirulence · 2026
    Article
  3. Drug-likeness prioritised selection identifies anti-Journal of enzyme inhibition and medicinal chemistry · 2026
    Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Review
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

124 more citing papers are in PubMed but not listed here.

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

3 authors.

Joseph M PaggiDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.
Ayush PanditDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.
Ron O DrorDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA.

Funding

Discovering the mechanism of GPCR-mediated arrestin stimulation to enable effective drug therapiesR01GM127359 · NIGMS · STANFORD UNIVERSITY · PI DROR, RON · 2018 to 2022
$1.5M
NIGMS NIH HHS R01 GM127359
6 · The paper itself

Abstract

Molecular docking has become an essential part of a structural biologist's and medicinal chemist's toolkits. Given a chemical compound and the three-dimensional structure of a molecular target-for example, a protein-docking methods fit the compound into the target, predicting the compound's bound structure and binding energy. Docking can be used to discover novel ligands for a target by screening large virtual compound libraries. Docking can also provide a useful starting point for structure-based ligand optimization or for investigating a ligand's mechanism of action. Advances in computational methods, including both physics-based and machine learning approaches, as well as in complementary experimental techniques, are making docking an even more powerful tool. We review how docking works and how it can drive drug discovery and biological research. We also describe its current limitations and ongoing efforts to overcome them.

Indexed as

Drug DiscoveryMolecular Docking SimulationProtein BindingProteinsBinding SitesDrug DesignHumansLigandsMachine LearningLigandsProteinsbiophysicscomputational protein–ligand dockingdrug discoverylead optimizationvirtual screening

Identifiers

PMID38594926
PMCPMC13198409

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.