Tokenized and continuous embedding compressions of protein sequence and structure Article Swipe

PDF

Amy X. Lu , Wilson Yan , Kevin Yang , Vladimir Gligorijević , Kyunghyun Cho , Pieter Abbeel , Richard Bonneau , Nathan C. Frey ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1016/j.patter.2025.101289

Related Topics

Computational Biology

Artificial Intelligence

Concepts

Sequence (biology) Embedding Computational biology Chemistry Computer science Biochemistry Biology Artificial intelligence

Metadata

Type: article
Language: en
Landing Page: https://doi.org/10.1016/j.patter.2025.101289
PDF: https://www.cell.com/action/showPdf?pii=S2666389925001370
OA Status: gold
Cited By: 2
References: 69
Related Works: 10
OpenAlex ID: https://openalex.org/W4411274741

All OpenAlex metadata

Raw OpenAlex JSON

OpenAlex ID: https://openalex.org/W4411274741

Canonical identifier for this work in OpenAlex
DOI: https://doi.org/10.1016/j.patter.2025.101289

Digital Object Identifier
Title: Tokenized and continuous embedding compressions of protein sequence and structure

Work title
Type: article

OpenAlex work type
Language: en

Primary language
Publication year: 2025

Year of publication
Publication date: 2025-06-01

Full publication date if available
Authors: Amy X. Lu, Wilson Yan, Kevin Yang, Vladimir Gligorijević, Kyunghyun Cho, Pieter Abbeel, Richard Bonneau, Nathan C. Frey

List of authors in order
Landing page: https://doi.org/10.1016/j.patter.2025.101289

Publisher landing page
PDF URL: https://www.cell.com/action/showPdf?pii=S2666389925001370

Direct link to full text PDF
Open access: Yes

Whether a free full text is available
OA status: gold

Open access status per OpenAlex
OA URL: https://www.cell.com/action/showPdf?pii=S2666389925001370

Direct OA link when available
Concepts: Sequence (biology), Embedding, Computational biology, Chemistry, Computer science, Biochemistry, Biology, Artificial intelligence

Top concepts (fields/topics) attached by OpenAlex
Cited by: 2

Total citation count in OpenAlex
Citations by year (recent): 2025: 2

Per-year citation counts (last 5 years)
References (count): 69

Number of works referenced by this work
Related works (count): 10

Other works algorithmically related by OpenAlex

Full payload

id	https://openalex.org/W4411274741
doi	https://doi.org/10.1016/j.patter.2025.101289
ids.doi	https://doi.org/10.1016/j.patter.2025.101289
ids.pmid	https://pubmed.ncbi.nlm.nih.gov/40575127
ids.openalex	https://openalex.org/W4411274741
fwci	5.36588926
type	article
title	Tokenized and continuous embedding compressions of protein sequence and structure
biblio.issue	6
biblio.volume	6
biblio.last_page	101289
biblio.first_page	101289
topics[0].id	https://openalex.org/T10044
topics[0].field.id	https://openalex.org/fields/13
topics[0].field.display_name	Biochemistry, Genetics and Molecular Biology
topics[0].score	0.9990000128746033
topics[0].domain.id	https://openalex.org/domains/1
topics[0].domain.display_name	Life Sciences
topics[0].subfield.id	https://openalex.org/subfields/1312
topics[0].subfield.display_name	Molecular Biology
topics[0].display_name	Protein Structure and Dynamics
topics[1].id	https://openalex.org/T10521
topics[1].field.id	https://openalex.org/fields/13
topics[1].field.display_name	Biochemistry, Genetics and Molecular Biology
topics[1].score	0.9965000152587891
topics[1].domain.id	https://openalex.org/domains/1
topics[1].domain.display_name	Life Sciences
topics[1].subfield.id	https://openalex.org/subfields/1312
topics[1].subfield.display_name	Molecular Biology
topics[1].display_name	RNA and protein synthesis mechanisms
topics[2].id	https://openalex.org/T11048
topics[2].field.id	https://openalex.org/fields/23
topics[2].field.display_name	Environmental Science
topics[2].score	0.9932000041007996
topics[2].domain.id	https://openalex.org/domains/3
topics[2].domain.display_name	Physical Sciences
topics[2].subfield.id	https://openalex.org/subfields/2303
topics[2].subfield.display_name	Ecology
topics[2].display_name	Bacteriophages and microbial interactions
funders[0].id	https://openalex.org/F4320334593
funders[0].ror	https://ror.org/01h531d29
funders[0].display_name	Natural Sciences and Engineering Research Council of Canada
is_xpac	False
apc_list.value	5200
apc_list.currency	USD
apc_list.value_usd	5200
apc_paid.value	5200
apc_paid.currency	USD
apc_paid.value_usd	5200
concepts[0].id	https://openalex.org/C2778112365
concepts[0].level	2
concepts[0].score	0.6464170217514038
concepts[0].wikidata	https://www.wikidata.org/wiki/Q3511065
concepts[0].display_name	Sequence (biology)
concepts[1].id	https://openalex.org/C41608201
concepts[1].level	2
concepts[1].score	0.5679190754890442
concepts[1].wikidata	https://www.wikidata.org/wiki/Q980509
concepts[1].display_name	Embedding
concepts[2].id	https://openalex.org/C70721500
concepts[2].level	1
concepts[2].score	0.44831186532974243
concepts[2].wikidata	https://www.wikidata.org/wiki/Q177005
concepts[2].display_name	Computational biology
concepts[3].id	https://openalex.org/C185592680
concepts[3].level	0
concepts[3].score	0.3789213299751282
concepts[3].wikidata	https://www.wikidata.org/wiki/Q2329
concepts[3].display_name	Chemistry
concepts[4].id	https://openalex.org/C41008148
concepts[4].level	0
concepts[4].score	0.35711967945098877
concepts[4].wikidata	https://www.wikidata.org/wiki/Q21198
concepts[4].display_name	Computer science
concepts[5].id	https://openalex.org/C55493867
concepts[5].level	1
concepts[5].score	0.22951766848564148
concepts[5].wikidata	https://www.wikidata.org/wiki/Q7094
concepts[5].display_name	Biochemistry
concepts[6].id	https://openalex.org/C86803240
concepts[6].level	0
concepts[6].score	0.21492645144462585
concepts[6].wikidata	https://www.wikidata.org/wiki/Q420
concepts[6].display_name	Biology
concepts[7].id	https://openalex.org/C154945302
concepts[7].level	1
concepts[7].score	0.1662244200706482
concepts[7].wikidata	https://www.wikidata.org/wiki/Q11660
concepts[7].display_name	Artificial intelligence
keywords[0].id	https://openalex.org/keywords/sequence
keywords[0].score	0.6464170217514038
keywords[0].display_name	Sequence (biology)
keywords[1].id	https://openalex.org/keywords/embedding
keywords[1].score	0.5679190754890442
keywords[1].display_name	Embedding
keywords[2].id	https://openalex.org/keywords/computational-biology
keywords[2].score	0.44831186532974243
keywords[2].display_name	Computational biology
keywords[3].id	https://openalex.org/keywords/chemistry
keywords[3].score	0.3789213299751282
keywords[3].display_name	Chemistry
keywords[4].id	https://openalex.org/keywords/computer-science
keywords[4].score	0.35711967945098877
keywords[4].display_name	Computer science
keywords[5].id	https://openalex.org/keywords/biochemistry
keywords[5].score	0.22951766848564148
keywords[5].display_name	Biochemistry
keywords[6].id	https://openalex.org/keywords/biology
keywords[6].score	0.21492645144462585
keywords[6].display_name	Biology
keywords[7].id	https://openalex.org/keywords/artificial-intelligence
keywords[7].score	0.1662244200706482
keywords[7].display_name	Artificial intelligence
language	en
locations[0].id	doi:10.1016/j.patter.2025.101289
locations[0].is_oa	True
locations[0].source.id	https://openalex.org/S4210198061
locations[0].source.issn	2666-3899
locations[0].source.type	journal
locations[0].source.is_oa	True
locations[0].source.issn_l	2666-3899
locations[0].source.is_core	True
locations[0].source.is_in_doaj	True
locations[0].source.display_name	Patterns
locations[0].source.host_organization	https://openalex.org/P4310320990
locations[0].source.host_organization_name	Elsevier BV
locations[0].source.host_organization_lineage	https://openalex.org/P4310320990
locations[0].source.host_organization_lineage_names	Elsevier BV
locations[0].license	cc-by
locations[0].pdf_url	https://www.cell.com/action/showPdf?pii=S2666389925001370
locations[0].version	publishedVersion
locations[0].raw_type	journal-article
locations[0].license_id	https://openalex.org/licenses/cc-by
locations[0].is_accepted	True
locations[0].is_published	True
locations[0].raw_source_name	Patterns
locations[0].landing_page_url	https://doi.org/10.1016/j.patter.2025.101289
locations[1].id	pmid:40575127
locations[1].is_oa	False
locations[1].source.id	https://openalex.org/S4306525036
locations[1].source.issn
locations[1].source.type	repository
locations[1].source.is_oa	False
locations[1].source.issn_l
locations[1].source.is_core	False
locations[1].source.is_in_doaj	False
locations[1].source.display_name	PubMed
locations[1].source.host_organization	https://openalex.org/I1299303238
locations[1].source.host_organization_name	National Institutes of Health
locations[1].source.host_organization_lineage	https://openalex.org/I1299303238
locations[1].license
locations[1].pdf_url
locations[1].version	publishedVersion
locations[1].raw_type
locations[1].license_id
locations[1].is_accepted	True
locations[1].is_published	True
locations[1].raw_source_name	Patterns (New York, N.Y.)
locations[1].landing_page_url	https://pubmed.ncbi.nlm.nih.gov/40575127
locations[2].id	pmh:oai:pubmedcentral.nih.gov:12191763
locations[2].is_oa	True
locations[2].source.id	https://openalex.org/S2764455111
locations[2].source.issn
locations[2].source.type	repository
locations[2].source.is_oa	False
locations[2].source.issn_l
locations[2].source.is_core	False
locations[2].source.is_in_doaj	False
locations[2].source.display_name	PubMed Central
locations[2].source.host_organization	https://openalex.org/I1299303238
locations[2].source.host_organization_name	National Institutes of Health
locations[2].source.host_organization_lineage	https://openalex.org/I1299303238
locations[2].license	other-oa
locations[2].pdf_url
locations[2].version	submittedVersion
locations[2].raw_type	Text
locations[2].license_id	https://openalex.org/licenses/other-oa
locations[2].is_accepted	False
locations[2].is_published	False
locations[2].raw_source_name	Patterns (N Y)
locations[2].landing_page_url	https://www.ncbi.nlm.nih.gov/pmc/articles/12191763
indexed_in	crossref, doaj, pubmed
authorships[0].author.id	https://openalex.org/A5023348845
authorships[0].author.orcid
authorships[0].author.display_name	Amy X. Lu
authorships[0].countries	US
authorships[0].affiliations[0].raw_affiliation_string	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[0].affiliations[1].institution_ids	https://openalex.org/I95457486
authorships[0].affiliations[1].raw_affiliation_string	University of California, Berkeley, Berkeley, CA, USA.
authorships[0].institutions[0].id	https://openalex.org/I95457486
authorships[0].institutions[0].ror	https://ror.org/01an7q238
authorships[0].institutions[0].type	education
authorships[0].institutions[0].lineage	https://openalex.org/I95457486
authorships[0].institutions[0].country_code	US
authorships[0].institutions[0].display_name	University of California, Berkeley
authorships[0].author_position	first
authorships[0].raw_author_name	Amy X Lu
authorships[0].is_corresponding	False
authorships[0].raw_affiliation_strings	Prescient Design, Genentech, South San Francisco, CA, USA., University of California, Berkeley, Berkeley, CA, USA.
authorships[1].author.id	https://openalex.org/A5051069937
authorships[1].author.orcid
authorships[1].author.display_name	Wilson Yan
authorships[1].countries	US
authorships[1].affiliations[0].institution_ids	https://openalex.org/I95457486
authorships[1].affiliations[0].raw_affiliation_string	University of California, Berkeley, Berkeley, CA, USA.
authorships[1].institutions[0].id	https://openalex.org/I95457486
authorships[1].institutions[0].ror	https://ror.org/01an7q238
authorships[1].institutions[0].type	education
authorships[1].institutions[0].lineage	https://openalex.org/I95457486
authorships[1].institutions[0].country_code	US
authorships[1].institutions[0].display_name	University of California, Berkeley
authorships[1].author_position	middle
authorships[1].raw_author_name	Wilson Yan
authorships[1].is_corresponding	False
authorships[1].raw_affiliation_strings	University of California, Berkeley, Berkeley, CA, USA.
authorships[2].author.id	https://openalex.org/A5101814676
authorships[2].author.orcid	https://orcid.org/0000-0001-7221-6642
authorships[2].author.display_name	Kevin Yang
authorships[2].countries	US
authorships[2].affiliations[0].institution_ids	https://openalex.org/I1290206253, https://openalex.org/I4400600948
authorships[2].affiliations[0].raw_affiliation_string	Microsoft Research New England, Cambridge, MA, USA.
authorships[2].institutions[0].id	https://openalex.org/I4400600948
authorships[2].institutions[0].ror	https://ror.org/010wkqn50
authorships[2].institutions[0].type	company
authorships[2].institutions[0].lineage	https://openalex.org/I1290206253, https://openalex.org/I4400600948
authorships[2].institutions[0].country_code
authorships[2].institutions[0].display_name	Microsoft Research New England (United States)
authorships[2].institutions[1].id	https://openalex.org/I1290206253
authorships[2].institutions[1].ror	https://ror.org/00d0nc645
authorships[2].institutions[1].type	company
authorships[2].institutions[1].lineage	https://openalex.org/I1290206253
authorships[2].institutions[1].country_code	US
authorships[2].institutions[1].display_name	Microsoft (United States)
authorships[2].author_position	middle
authorships[2].raw_author_name	Kevin K Yang
authorships[2].is_corresponding	False
authorships[2].raw_affiliation_strings	Microsoft Research New England, Cambridge, MA, USA.
authorships[3].author.id	https://openalex.org/A5061943951
authorships[3].author.orcid	https://orcid.org/0000-0002-5165-0973
authorships[3].author.display_name	Vladimir Gligorijević
authorships[3].affiliations[0].raw_affiliation_string	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[3].author_position	middle
authorships[3].raw_author_name	Vladimir Gligorijevic
authorships[3].is_corresponding	False
authorships[3].raw_affiliation_strings	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[4].author.id	https://openalex.org/A5091175785
authorships[4].author.orcid	https://orcid.org/0000-0003-1669-3211
authorships[4].author.display_name	Kyunghyun Cho
authorships[4].countries	US
authorships[4].affiliations[0].institution_ids	https://openalex.org/I57206974
authorships[4].affiliations[0].raw_affiliation_string	New York University, New York City, NY, USA.
authorships[4].affiliations[1].raw_affiliation_string	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[4].institutions[0].id	https://openalex.org/I57206974
authorships[4].institutions[0].ror	https://ror.org/0190ak572
authorships[4].institutions[0].type	education
authorships[4].institutions[0].lineage	https://openalex.org/I57206974
authorships[4].institutions[0].country_code	US
authorships[4].institutions[0].display_name	New York University
authorships[4].author_position	middle
authorships[4].raw_author_name	Kyunghyun Cho
authorships[4].is_corresponding	False
authorships[4].raw_affiliation_strings	New York University, New York City, NY, USA., Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[5].author.id	https://openalex.org/A5049349154
authorships[5].author.orcid
authorships[5].author.display_name	Pieter Abbeel
authorships[5].countries	US
authorships[5].affiliations[0].institution_ids	https://openalex.org/I95457486
authorships[5].affiliations[0].raw_affiliation_string	University of California, Berkeley, Berkeley, CA, USA.
authorships[5].institutions[0].id	https://openalex.org/I95457486
authorships[5].institutions[0].ror	https://ror.org/01an7q238
authorships[5].institutions[0].type	education
authorships[5].institutions[0].lineage	https://openalex.org/I95457486
authorships[5].institutions[0].country_code	US
authorships[5].institutions[0].display_name	University of California, Berkeley
authorships[5].author_position	middle
authorships[5].raw_author_name	Pieter Abbeel
authorships[5].is_corresponding	False
authorships[5].raw_affiliation_strings	University of California, Berkeley, Berkeley, CA, USA.
authorships[6].author.id	https://openalex.org/A5055203249
authorships[6].author.orcid	https://orcid.org/0000-0003-4354-7906
authorships[6].author.display_name	Richard Bonneau
authorships[6].affiliations[0].raw_affiliation_string	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[6].author_position	middle
authorships[6].raw_author_name	Richard Bonneau
authorships[6].is_corresponding	False
authorships[6].raw_affiliation_strings	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[7].author.id	https://openalex.org/A5090160831
authorships[7].author.orcid	https://orcid.org/0000-0001-5291-6131
authorships[7].author.display_name	Nathan C. Frey
authorships[7].affiliations[0].raw_affiliation_string	Prescient Design, Genentech, South San Francisco, CA, USA.
authorships[7].author_position	last
authorships[7].raw_author_name	Nathan C Frey
authorships[7].is_corresponding	False
authorships[7].raw_affiliation_strings	Prescient Design, Genentech, South San Francisco, CA, USA.
has_content.pdf	True
has_content.grobid_xml	True
is_paratext	False
open_access.is_oa	True
open_access.oa_url	https://www.cell.com/action/showPdf?pii=S2666389925001370
open_access.oa_status	gold
open_access.any_repository_has_fulltext	False
created_date	2025-10-10T00:00:00
display_name	Tokenized and continuous embedding compressions of protein sequence and structure
has_fulltext	False
is_retracted	False
updated_date	2025-11-06T03:46:38.306776
primary_topic.id	https://openalex.org/T10044
primary_topic.field.id	https://openalex.org/fields/13
primary_topic.field.display_name	Biochemistry, Genetics and Molecular Biology
primary_topic.score	0.9990000128746033
primary_topic.domain.id	https://openalex.org/domains/1
primary_topic.domain.display_name	Life Sciences
primary_topic.subfield.id	https://openalex.org/subfields/1312
primary_topic.subfield.display_name	Molecular Biology
primary_topic.display_name	Protein Structure and Dynamics
related_works	https://openalex.org/W4387497383, https://openalex.org/W2948807893, https://openalex.org/W2899084033, https://openalex.org/W2778153218, https://openalex.org/W2748952813, https://openalex.org/W1531601525, https://openalex.org/W4391375266, https://openalex.org/W2078814861, https://openalex.org/W2527526854, https://openalex.org/W2966686650
cited_by_count	2
counts_by_year[0].year	2025
counts_by_year[0].cited_by_count	2
locations_count	3
best_oa_location.id	doi:10.1016/j.patter.2025.101289
best_oa_location.is_oa	True
best_oa_location.source.id	https://openalex.org/S4210198061
best_oa_location.source.issn	2666-3899
best_oa_location.source.type	journal
best_oa_location.source.is_oa	True
best_oa_location.source.issn_l	2666-3899
best_oa_location.source.is_core	True
best_oa_location.source.is_in_doaj	True
best_oa_location.source.display_name	Patterns
best_oa_location.source.host_organization	https://openalex.org/P4310320990
best_oa_location.source.host_organization_name	Elsevier BV
best_oa_location.source.host_organization_lineage	https://openalex.org/P4310320990
best_oa_location.source.host_organization_lineage_names	Elsevier BV
best_oa_location.license	cc-by
best_oa_location.pdf_url	https://www.cell.com/action/showPdf?pii=S2666389925001370
best_oa_location.version	publishedVersion
best_oa_location.raw_type	journal-article
best_oa_location.license_id	https://openalex.org/licenses/cc-by
best_oa_location.is_accepted	True
best_oa_location.is_published	True
best_oa_location.raw_source_name	Patterns
best_oa_location.landing_page_url	https://doi.org/10.1016/j.patter.2025.101289
primary_location.id	doi:10.1016/j.patter.2025.101289
primary_location.is_oa	True
primary_location.source.id	https://openalex.org/S4210198061
primary_location.source.issn	2666-3899
primary_location.source.type	journal
primary_location.source.is_oa	True
primary_location.source.issn_l	2666-3899
primary_location.source.is_core	True
primary_location.source.is_in_doaj	True
primary_location.source.display_name	Patterns
primary_location.source.host_organization	https://openalex.org/P4310320990
primary_location.source.host_organization_name	Elsevier BV
primary_location.source.host_organization_lineage	https://openalex.org/P4310320990
primary_location.source.host_organization_lineage_names	Elsevier BV
primary_location.license	cc-by
primary_location.pdf_url	https://www.cell.com/action/showPdf?pii=S2666389925001370
primary_location.version	publishedVersion
primary_location.raw_type	journal-article
primary_location.license_id	https://openalex.org/licenses/cc-by
primary_location.is_accepted	True
primary_location.is_published	True
primary_location.raw_source_name	Patterns
primary_location.landing_page_url	https://doi.org/10.1016/j.patter.2025.101289
publication_date	2025-06-01
publication_year	2025
referenced_works	https://openalex.org/W2130479394, https://openalex.org/W2102461176, https://openalex.org/W3177828909, https://openalex.org/W4327550249, https://openalex.org/W4296032638, https://openalex.org/W6810245500, https://openalex.org/W4392381140, https://openalex.org/W6800751262, https://openalex.org/W6850045305, https://openalex.org/W3177500196, https://openalex.org/W6739901393, https://openalex.org/W6868855459, https://openalex.org/W6870615235, https://openalex.org/W6968058152, https://openalex.org/W6936386102, https://openalex.org/W6863030648, https://openalex.org/W6791955017, https://openalex.org/W6687483927, https://openalex.org/W6803536264, https://openalex.org/W6810595431, https://openalex.org/W6779823529, https://openalex.org/W6783713337, https://openalex.org/W6787283782, https://openalex.org/W6810985806, https://openalex.org/W6803870738, https://openalex.org/W6762931180, https://openalex.org/W3106745904, https://openalex.org/W3095583226, https://openalex.org/W6869482409, https://openalex.org/W6865088576, https://openalex.org/W6868365405, https://openalex.org/W2752796333, https://openalex.org/W6838437557, https://openalex.org/W3025427857, https://openalex.org/W6776218486, https://openalex.org/W6852843773, https://openalex.org/W6857461762, https://openalex.org/W6839106506, https://openalex.org/W6861371584, https://openalex.org/W2118265845, https://openalex.org/W6838639034, https://openalex.org/W6838088261, https://openalex.org/W6690026940, https://openalex.org/W3121370741, https://openalex.org/W4281485151, https://openalex.org/W1607198972, https://openalex.org/W4236965008, https://openalex.org/W2971074500, https://openalex.org/W2963799213, https://openalex.org/W1583837637, https://openalex.org/W4387158294, https://openalex.org/W4399618913, https://openalex.org/W2242818861, https://openalex.org/W4399115900, https://openalex.org/W4399114836, https://openalex.org/W3209873929, https://openalex.org/W4280528743, https://openalex.org/W4391652655, https://openalex.org/W4406440058, https://openalex.org/W4281719345, https://openalex.org/W4394930608, https://openalex.org/W4392271820, https://openalex.org/W4280491725, https://openalex.org/W4320855461, https://openalex.org/W4365800072, https://openalex.org/W4385245566, https://openalex.org/W4287802874, https://openalex.org/W3195577433, https://openalex.org/W3036167779
referenced_works_count	69
abstract_inverted_index
cited_by_percentile_year.max	97
cited_by_percentile_year.min	95
countries_distinct_count	1
institutions_distinct_count	8
citation_normalized_percentile.value	0.90412429
citation_normalized_percentile.is_in_top_1_percent	False
citation_normalized_percentile.is_in_top_10_percent	True