Evidence map›Paper›PMID 42462965›Full record

ReviewJournal of molecular biology2026

The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.

Pradeep Bk, Shi-Jie Chen, Ruxandra Dima, Mubasher Hassan, Andrzej Joachimiak, Daisuke Kihara, Andrzej Kloczkowski, Jeffrey Law, Adam Liwo, Jarek Meller and 13 more

Abstract readReview
In one paragraph

Review in Journal of molecular biology, 2026. 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

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

23 authors.

Pradeep BkIowa State University, United States.
Shi-Jie ChenUniversity of Missouri-Columbia, United States.
Ruxandra DimaUniversity of Cincinnati, United States.
Mubasher HassanNationwide Children's Hospital, United States.
Andrzej JoachimiakUniversity of Chicago and Argonne National Lab, United States.
Daisuke KiharaPurdue University, United States.
Andrzej KloczkowskiNationwide Children's Hospital, United States.
Jeffrey LawNational Renewable Energy Lab (Lab of the Rockies), United States.
Adam LiwoUniversity of Gdańsk, Poland.
Jarek MellerUniversity of Cincinnati, United States.
Cristan MichelettiInternational School for Advanced Studies (SISSA), Trieste, Italy.
Wladek MinorUniversity of Virginia, United States.
Gaetano T MontelioneRensselaer Polytechnic Institute, United States.
Shalom RackovskyUniversity of Rochester School of Medicine and Dentistry, United States.
Domenico ScaramozzinoKarolinska Institutet, Sweden.
Miki SendaKEK High Energy Accelerator Research Organization, Japan.
Toshiya SendaKEK High Energy Accelerator Research Organization, Japan.
Jeffrey SkolnickGeorgia Institute of Technology, United States.
George StanUniversity of Cincinnati, United States.
Ilya A VakserUniversity of Kansas, United States.
Jin WangStony Brook University, United States.
Xiaoqin ZouUniversity of Missouri-Columbia, United States.
Robert L JerniganIowa State University, United States. Electronic address: jernigan@iastate.edu.

Funding

Center for Structural Biology of HIV RNAU54AI170660 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALICE TELESNITSKY · 2022 to 2026
$32.1M
TO PROVIDE SCIENTIFIC SUPPORT TO THE CENTERS FOR RESEARCH ON STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES.75N93022C00035 · NIAID · NORTHWESTERN UNIVERSITY AT CHICAGO · PI SATCHELL, KARLA · 2022 to 2025
$20.7M
INTERNAL BONDIN IN PROTEINSR01GM014312 · NIGMS · CORNELL UNIVERSITY ITHACA · PI MAISURADZE, GIA, RACKOVSKY, SHALOM R · 1985 to 2021
$9.4M
Purchase of a GPU cluster for deep learning applications in protein-protein interaction and supercomplex prediction and biochemical literature annotation.R35GM118039 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI JEFFREY SKOLNICK · 2016 to 2026
$5.8M
New methods for computational modeling of RNA structuresR35GM134919 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI SHI-JIE CHEN · 2020 to 2026
$3.3M
Hybrid Methods for Dynamic Structure Analysis of Proteins from Pathogenic MicroorganismsR35GM141818 · NIGMS · RENSSELAER POLYTECHNIC INSTITUTE · PI MONTELIONE, GAETANO T · 2021 to 2025
$3.3M
Structure prediction and in silico screening of protein-peptide interactionsR35GM136409 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI XIAOQIN ZOU · 2020 to 2026
$2.9M
Novel Use of Genome Information to Understand MutationsR01HG012117 · NHGRI · IOWA STATE UNIVERSITY · PI JERNIGAN, ROBERT L, KLOCZKOWSKI, ANDRZEJ · 2021 to 2025
$2.3M
Data-driven biomolecular structure modeling for cryo-EM mapsR35GM158267 · NIGMS · PURDUE UNIVERSITY · PI Daisuke Kihara · 2025 to 2026
$791k
Modeling of macromolecular interactions in the cellR35GM156453 · NIGMS · UNIVERSITY OF KANSAS LAWRENCE · PI ILYA VAKSER · 2025 to 2026
$671k
An effective statistical inference framework to develop innovative compensations for protein mutationsR01GM157600 · NIGMS · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Zhao Ren · 2024 to 2026
$611k
NHGRI NIH HHS R01 HG012117NIAID NIH HHS U54 AI170660NIGMS NIH HHS R01 GM014312NIGMS NIH HHS R01 GM157600NIGMS NIH HHS R35 GM118039NIGMS NIH HHS R35 GM134919NIGMS NIH HHS R35 GM136409NIGMS NIH HHS R35 GM141818NIGMS NIH HHS R35 GM156453NIGMS NIH HHS R35 GM158267NIH HHS 75N93022C00035
6 · The paper itself

Abstract

The ability to understand proteins and their behaviors has been drastically improved by major successes in structure prediction and the appearance of Large Protein Language Models (LPLMs). The speed with which Deep Learning and Artificial Intelligence are now affecting computational protein studies is remarkable, but there are now many opportunities for further rapid progress with applications of these methods. Rapid gains are likely to come from studies using the approaches identified in this perspective. Addressing and predicting ligand-binding sites in protein structures, as well as the prediction of reliable structures of proteins interacting with other proteins, will be pivotal for learning the full details of structural mechanisms and dynamics. The prediction of multi-state protein ensembles, conformational transitions, dynamics of large protein complexes, and integration with experimental data is likely to happen quickly.

Indexed as

Artificial IntelligenceComputational BiologyProteinsBinding SitesHumansModels, MolecularProtein ConformationProteinsdisordered proteinsintegrating predicted structures with experimental datalarge protein language modelspredicted protein structures and ensemblesprotein interactions

Identifiers

PMID42462965
PMCPMC13564473

What OpenQuestion holds

Textmetadata
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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.