Evidence map›Paper›PMID 38187536›Full record

ArticlebioRxiv : the preprint server for biology2024

AlphaFold2 structures template ligand discovery.

Jiankun Lyu, Nicholas Kapolka, Ryan Gumpper, Assaf Alon, Liang Wang, Manish K Jain, Ximena Barros-Álvarez, Kensuke Sakamoto, Yoojoong Kim, Jeffrey DiBerto and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Jiankun LyuDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Nicholas KapolkaDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Ryan GumpperDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Assaf AlonDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
Liang WangDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Manish K JainDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Ximena Barros-ÁlvarezDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Kensuke SakamotoDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Yoojoong KimDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Jeffrey DiBertoDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Kuglae KimDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.
Tia A TumminoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0000-0001-9155-820X
Sijie HuangDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
John J IrwinDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Olga O TarkhanovaChemspace LLC, Kyiv, 02094, Ukraine.
Yurii MorozChemspace LLC, Kyiv, 02094, Ukraine.
Georgios SkiniotisDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Andrew C KruseDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
Brian K ShoichetDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Bryan L RothDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599-7365, USA.

Funding

Development and Testing of New Computational Methods for Ligand Discovery and MechanismR35GM122481 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Brian K Shoichet · 2017 to 2026
$8.5M
Molecular Details of Psychoactive Drug ActionsR01MH112205 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Bryan L. Roth, Brian K Shoichet · 2017 to 2026
$6.1M
A Web-Based Automatic Virtual Screening SystemR01GM071896 · NIGMS · UNIVERSITY OF TORONTO · PI IRWIN, JOHN J. · 2004 to 2024
$6.0M
Mechanistic insights into LSD actions at 5-HT2A serotonin receptorsR37DA045657 · NIDA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Bryan L. Roth · 2018 to 2026
$5.8M
Ultra-large library docking for ligand discoveryR01GM133836 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI IRWIN, JOHN J. · 2019 to 2022
$1.6M
Molecular mechanisms of sigma receptor signalingR01GM119185 · NIGMS · HARVARD MEDICAL SCHOOL · PI KRUSE, ANDREW · 2017 to 2020
$1.3M
NIDA NIH HHS R37 DA045657NIGMS NIH HHS R01 GM071896NIGMS NIH HHS R01 GM119185NIGMS NIH HHS R01 GM133836NIGMS NIH HHS R35 GM122481NIMH NIH HHS R01 MH112205
6 · The paper itself

Abstract

AlphaFold2 (AF2) and RosettaFold have greatly expanded the number of structures available for structure-based ligand discovery, even though retrospective studies have cast doubt on their direct usefulness for that goal. Here, we tested unrefined AF2 models

Identifiers

PMID38187536
PMCPMC10769324

What OpenQuestion holds

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Registered trials

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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.