Evidence map›Paper›PMID 42618805›Full record

ArticleNature biotechnology2026

A blinded, prospective benchmark of in silico antibody discovery anchored to experimental affinity and developability.

M Frank Erasmus, Daniel Bedinger, Elizabeth Hopkins, Ginger Ferguson, Justine Strickler, Christilyn P Graff, Samantha R Summers, Stacy L Capehart, Joshua D Slocum, Crystal Richardson and 107 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

117 authors.

M Frank ErasmusSpecifica, an IQVIA Business, Santa Fe, NM, USA. mfrank.erasmus@iqvia.com.ORCID http://orcid.org/0000-0002-8046-5048
Daniel BedingerCarterra, Salt Lake City, UT, USA.ORCID http://orcid.org/0000-0001-5009-9369
Elizabeth HopkinsSapidyne Instruments, Inc. GmbH, Boise, ID, USA.
Ginger FergusonSapidyne Instruments, Inc. GmbH, Boise, ID, USA.
Justine StricklerSapidyne Instruments, Inc. GmbH, Boise, ID, USA.
Christilyn P GraffMosaic Biosciences, Boulder, CO, USA.
Samantha R SummersMosaic Biosciences, Boulder, CO, USA.
Stacy L CapehartMosaic Biosciences, Boulder, CO, USA.
Joshua D SlocumMosaic Biosciences, Boulder, CO, USA.
Crystal RichardsonGENEWIZ, Azenta Life Sciences, South Plainfield, NJ, USA.
Sumit KumarGENEWIZ, Azenta Life Sciences, South Plainfield, NJ, USA.
Zhifei SunGENEWIZ, Azenta Life Sciences, South Plainfield, NJ, USA.
Yujie ShangGENEWIZ, Azenta Life Sciences, South Plainfield, NJ, USA.
Jixian ZhangAureka Biotechnologies, Laguna Hills, CA, USA.
Ming GuAureka Biotechnologies, Laguna Hills, CA, USA.
Lixia YiAureka Biotechnologies, Laguna Hills, CA, USA.
Alon WellnerAureka Biotechnologies, Laguna Hills, CA, USA.
Shuangjia ZhengAureka Biotechnologies, Laguna Hills, CA, USA.ORCID http://orcid.org/0000-0001-9747-4285
Wei LuAureka Biotechnologies, Laguna Hills, CA, USA.ORCID http://orcid.org/0000-0002-1572-2909
Pietro SormanniUniversity of Cambridge, Cambridge, UK.ORCID http://orcid.org/0000-0002-6228-2221
Matthew GreenigUniversity of Cambridge, Cambridge, UK.
Haiping ZhangShenzhen University of Advanced Technology (SUAT), Shenzhen, China.ORCID http://orcid.org/0000-0003-2133-1768
Brendan T MannThe George Washington University, Washington, D.C., USA.ORCID http://orcid.org/0000-0003-0694-7353
Mahdi BaghbanzadehThe George Washington University, Washington, D.C., USA.
Ali RahnavardThe George Washington University, Washington, D.C., USA.ORCID http://orcid.org/0000-0002-9710-0248
Gregory L MooreXencor, Inc., Pasadena, CA, USA.
Huaiyu SunXencor, Inc., Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-7181-8112
Ying DingXencor, Inc., Pasadena, CA, USA.
Alex NisthalXencor, Inc., Pasadena, CA, USA.
Jitendra KanodiaXencor, Inc., Pasadena, CA, USA.
Matthew J BernettXencor, Inc., Pasadena, CA, USA.
Aurélien PélissierBiomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-6638-5829
Yanjun ShaoBiomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA.
Maria Rodriguez MartinezBiomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-3766-4233
Karthik RameshIncyte, Inc., Wilmington, DE, USA.
Horacio NastriIncyte, Inc., Wilmington, DE, USA.ORCID http://orcid.org/0000-0002-0025-5930
Andreas EversMerck KGaA, Darmstadt, Germany.ORCID http://orcid.org/0000-0003-4643-1941
Anhar AbdelatifBristol-Myers Squibb, Princeton, NJ, USA.ORCID http://orcid.org/0009-0003-6476-2469
Andrew J BordnerBristol-Myers Squibb, Princeton, NJ, USA.
Mykola BordyuhBristol-Myers Squibb, Princeton, NJ, USA.
Lim HeoBristol-Myers Squibb, Princeton, NJ, USA.ORCID http://orcid.org/0000-0002-3153-2363
Brian A KiddBristol-Myers Squibb, Princeton, NJ, USA.ORCID http://orcid.org/0000-0003-2110-1145
H Serhat TetikolBristol-Myers Squibb, Princeton, NJ, USA.
Shuai WeiBristol-Myers Squibb, Princeton, NJ, USA.
Jung-Eun ShinSeismic Therapeutic, Watertown, MA, USA.
Ryan PecknerSeismic Therapeutic, Watertown, MA, USA.
Leigh ManleySeismic Therapeutic, Watertown, MA, USA.
Ajitesh LungeLocksmith Bio, Dover, DE, USA.
Yashas DevasurmuttLocksmith Bio, Dover, DE, USA.
Bora GulogluInstaDeep, London, UK.
Liviu CopoiuInstaDeep, London, UK.
Miles McGibbonInstaDeep, London, UK.
Monica L Fernandez-QuinteroScripps Research Institute, San Diego, CA, USA.
Nitesh MishraScripps Research Institute, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-5387-0486
Sean M CallaghanScripps Research Institute, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-2966-994X
Olivia M SwansonScripps Research Institute, San Diego, CA, USA.ORCID http://orcid.org/0000-0001-8162-8358
Daniel L V BaderScripps Research Institute, San Diego, CA, USA.
James A FergusonScripps Research Institute, San Diego, CA, USA.
Sai S R RaghavanScripps Research Institute, San Diego, CA, USA.
Benjamin NemozScripps Research Institute, San Diego, CA, USA.
Colleen A MaillieScripps Research Institute, San Diego, CA, USA.
Charles BowmanScripps Research Institute, San Diego, CA, USA.
Bryan BrineyScripps Research Institute, San Diego, CA, USA.ORCID http://orcid.org/0000-0001-9535-2866
Andrew B WardScripps Research Institute, San Diego, CA, USA.ORCID http://orcid.org/0000-0001-7153-3769
Paolo MarcatiliNovo Nordisk A/S, Bagsværd, Denmark.
Rahmad AkbarNovo Nordisk A/S, Bagsværd, Denmark.
Bing HeTencent AI for Life Sciences Lab, Shenzhen, China.ORCID http://orcid.org/0000-0003-1719-9290
Fandi WuTencent AI for Life Sciences Lab, Shenzhen, China.
Jianhua YaoTencent AI for Life Sciences Lab, Shenzhen, China.ORCID http://orcid.org/0000-0001-9157-9596
Bin HuLos Alamos National Laboratories, Los Alamos, NM, USA.ORCID http://orcid.org/0000-0002-0278-8466
Michal KucerLos Alamos National Laboratories, Los Alamos, NM, USA.
Kaetlyn Rose GibsonLos Alamos National Laboratories, Los Alamos, NM, USA.ORCID http://orcid.org/0009-0007-9838-0361
Rahul SomasundaramLos Alamos National Laboratories, Los Alamos, NM, USA.
Li-Wei HungLos Alamos National Laboratories, Los Alamos, NM, USA.ORCID http://orcid.org/0000-0001-6690-8458
Tomasz KaszubaWashington University in St. Louis, St. Louis, MO, USA.
Daved H FremontWashington University in St. Louis, St. Louis, MO, USA.
Hyeongsun JeongBioNote, Hwaseong-si, South Korea.
Vinodh Babu KurellaTakeda, Inc., Cambridge, MA, USA.
Shipra MalhotraTakeda, Inc., Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-2234-191X
Satyendra KumarTakeda, Inc., Cambridge, MA, USA.
Yanyun LiuZymo Research, Irvine, CA, USA.
Lingling XuZymo Research, Irvine, CA, USA.
Joshua MisaZymo Research, Irvine, CA, USA.ORCID http://orcid.org/0000-0002-3722-8573
Alexander Nicholas St JohnApoha, London, UK.
Jeff VogtJohns Hopkins University, Baltimore, MD, USA.
Fátima A Dávila-HernándezJohns Hopkins University, Baltimore, MD, USA.
Da XuJohns Hopkins University, Baltimore, MD, USA.
Michael ChungyounJohns Hopkins University, Baltimore, MD, USA.
Zyaja D HugganJohns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0009-0008-9497-5023
Jeffrey J GrayJohns Hopkins University, Baltimore, MD, USA.
Jonathan ParkinsonUniversity of California, San Diego, CA, USA.
Young Su KoUniversity of California, San Diego, CA, USA.
Wei WangUniversity of California, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-4377-5060
Franziska GeigerCradle, Zürich, Switzerland.
Jonathon D ZieglerCradle, Zürich, Switzerland.ORCID http://orcid.org/0009-0000-4730-7315
Nikhil HaasBioLM, Oakland, CA, USA.ORCID http://orcid.org/0009-0001-3389-7649
Chance ChallacombeBioLM, Oakland, CA, USA.
Ahmad QamarBioLM, Oakland, CA, USA.
Akshita SinghUTHealth, Houston, TX, USA.
Yi-Ching TangUTHealth, Houston, TX, USA.
Zhiqiang AnUTHealth, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9309-2335
Xiaoqian JiangUTHealth, Houston, TX, USA.ORCID http://orcid.org/0000-0001-9933-2205
Yejin KimUTHealth, Houston, TX, USA.ORCID http://orcid.org/0000-0001-7815-6310
Xinyan ZhaoUTHealth, Houston, TX, USA.
Erik SwansonManifold Bio, Boston, MA, USA.
Jürgen KlattigProBioGen, Berlin, Germany.
Karsten WinklerProBioGen, Berlin, Germany.
Tschimegma BataaProBioGen, Berlin, Germany.
Volker SandigProBioGen, Berlin, Germany.
Lilian DenzlerInstitute of Computational Life Sciences, Zurich University of Applied Sciences (ZHAW), Zurich, Switzerland.
Chunan LiuStructural and Molecular Biology, Division of Biosciences, University College, London, UK.ORCID http://orcid.org/0000-0001-5957-4197
Randall J BrezskiThe Antibody Society, Framingham, MA, USA.
Laura SpectorSpecifica, an IQVIA Business, Santa Fe, NM, USA.
Katheryn Perea-SchmittleSpecifica, an IQVIA Business, Santa Fe, NM, USA.
Sara D'AngeloSpecifica, an IQVIA Business, Santa Fe, NM, USA.
Fortunato FerraraSpecifica, an IQVIA Business, Santa Fe, NM, USA.
Andrew R M BradburySpecifica, an IQVIA Business, Santa Fe, NM, USA. andrew.bradbury@iqvia.com.ORCID http://orcid.org/0000-0002-5567-8172

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Experimentally validated prospective, blinded benchmarks are needed to separate durable advances from hype in computational antibody design. Here AIntibody, a challenge inspired by the Critical Assessment of Structure Prediction, tests 511 artificial intelligence (AI)-designed or predicted antibodies from 29 organizations on three tasks: in silico affinity maturation from phase 1 sequencing outputs, affinity ranking within heavy-chain complementarity-determining region 3 (HCDR3) clusters of a selection output and CDR design of proteins not included in a selection output. Validated with diverse experimental assays, several groups produced developable antibodies with affinities <100 pM. However, these successes were exceptions that did not transfer across tasks. Affinity-matured antibodies were modeled effectively. Except for one model, predicting high-affinity clones from clustered HCDR3 datasets was worse than random clone picking. Out-of-library design was highly variable for most method submissions, with many failing to outperform standard selections. The AIntibody challenge shows that AI can optimize antibodies in defined, biologically grounded regimes, in addition to highlighting critical gaps including affinity prediction and library-inspired antibody design and cross-task generalization.

Identifiers

PMID42618805

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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.