Evidence map›Paper›PMID 41833937›Full record

ArticleNature communications2026

Mining antibody functionality via AI-guided structural landscape profiling.

Stanislav S Terekhov, Nikita V Ivanisenko, Nan Zhang, Yuliana A Mokrushina, Dmitry E Nolde, Yakov A Lomakin, Arthur Zalevsky, Leyla A Ovchinnikova, Diana M Malabuiok, Margarita N Baranova and 25 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 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

35 authors.

Stanislav S Terekhov *Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0003-2220-0452
Nikita V Ivanisenko *Bioinformatics research group, AXXX, Moscow, Russia.
Nan Zhang *State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.ORCID http://orcid.org/0000-0002-5796-8851
Yuliana A Mokrushina *Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Dmitry E NoldeShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-3328-0024
Yakov A LomakinShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-3514-5395
Arthur ZalevskyShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0001-6987-8119
Leyla A OvchinnikovaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Diana M MalabuiokShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0009-0005-7740-282X
Margarita N BaranovaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Tatiana Shashkova *Bioinformatics research group, AXXX, Moscow, Russia.
Elena AliperShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Mingxiu ZhangState Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
Kun GuoState Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
Sergey DugaBioinformatics research group, AXXX, Moscow, Russia.
Nikolay AkhmetyanovBioinformatics research group, AXXX, Moscow, Russia.
Stepan MamontovBioinformatics research group, AXXX, Moscow, Russia.
Anastasia O SmirnovaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-7546-7436
Ilgar MamedovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-3992-9285
Tatiana V BobikShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Nikita N KostinShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0001-9447-9961
Aleksandr S ChernovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Igor E EliseevShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-3344-2513
Igor YaroshevichShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.ORCID http://orcid.org/0000-0002-8525-5568
Vitali M BoitsovAlferov University, Saint Petersburg, Russia.
Alexey V StepanovDepartment of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1616-4408
Ding ZhangDepartment of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Roman G EfremovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Ivan V SmirnovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.
Olga KardymonBioinformatics research group, AXXX, Moscow, Russia.
Hongkai ZhangState Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.ORCID http://orcid.org/0000-0003-2186-5508
Yu GuoState Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China. guoyu@nankai.edu.cn.ORCID http://orcid.org/0000-0002-8109-7515
Richard LernerDepartment of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
Alexander G GabibovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia. gabibov@gmail.com.ORCID http://orcid.org/0000-0001-8665-3288
Roger D KornbergStructural Biology, School of Medicine, Stanford University, Stanford, CA, USA. kornberg@stanford.edu.ORCID http://orcid.org/0000-0002-2425-7519

Funding

National Natural Science Foundation of China (National Science Foundation of China) 32271256National Natural Science Foundation of China (National Science Foundation of China) 82261138553
6 · The paper itself

Abstract

Despite substantial progress in single-cell screening techniques, antibody (Ab) repertoires still remain enigmatic. Here we show that Ab sequences can be linked to their functionality by using big data obtained from high-throughput sequencing. Using the expansive SARS-CoV-2 pandemic data, we develop an AI-based method to reveal the neutralization potential of Ab repertoires. We employ machine learning to process public 3D structural data of Ab-RBD complexes and create a comprehensive tool, RBD-AIM ( https://rbdaim.2a2i.org/ ), for high-throughput prediction of structural Ab epitopes based on Ab sequence. Using RBD-AIM, we analyze the local big data sources to evaluate the functional biodiversity of native B cell repertoires raised after vaccination and reconstructed in a yeast display system using single-cell microfluidics. This pipeline allows for rapid isolation of neutralizing Abs that promote the survival of transgenic hACE2+ mice in lethal models of SARS-CoV-2 infection. We believe that the AI-guided sequence-functionality link can be successfully employed for further high-throughput discovery of therapeutic Abs and functional analysis of Ab repertoires.

Indexed as

Antibodies, NeutralizingAntibodies, ViralCOVID-19SARS-CoV-2AnimalsArtificial IntelligenceB-LymphocytesData MiningEpitopesHigh-Throughput Nucleotide SequencingHumansMachine LearningMiceMice, TransgenicSpike Glycoprotein, CoronavirusAntibodies, NeutralizingAntibodies, ViralEpitopesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2

Identifiers

PMID41833937
PMCPMC13136481

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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.