S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure Article Swipe
Duolin Wang
,
Mahdi Pourmirzaei
,
Usman L. Abbas
,
Shuai Zeng
,
Negin Manshour
,
Farzaneh Esmaili
,
Biplab Poudel
,
Yuexu Jiang
,
Qing Shao
,
Jin Chen
,
Dong Xu
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/advs.202404212
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/advs.202404212
Proteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein functions and the design of proteins with the desired functions. The prediction and design capacity of PLMs relies on the representation gained from the protein sequences. However, the lack of crucial 3D structure information in most PLMs restricts the prediction capacity of PLMs in various applications, especially those heavily dependent on 3D structures. To address this issue, S‐PLM is introduced as a 3D structure‐aware PLM that utilizes multi‐view contrastive learning to align the sequence and 3D structure of a protein in a coordinated latent space. S‐PLM applies Swin‐Transformer on AlphaFold‐predicted protein structures to embed the structural information and fuses it into sequence‐based embedding from ESM2. Additionally, a library of lightweight tuning tools is provided to adapt S‐PLM for diverse downstream protein prediction tasks. The results demonstrate S‐PLM's superior performance over sequence‐only PLMs on all protein clustering and classification tasks, achieving competitiveness comparable to state‐of‐the‐art methods requiring both sequence and structure inputs. S‐PLM and its lightweight tuning tools are available at https://github.com/duolinwang/S-PLM/ .
Related Topics
Concepts
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/advs.202404212
- OA Status
- gold
- Cited By
- 17
- References
- 28
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4405330335
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4405330335Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1002/advs.202404212Digital Object Identifier
- Title
-
S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and StructureWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-12-12Full publication date if available
- Authors
-
Duolin Wang, Mahdi Pourmirzaei, Usman L. Abbas, Shuai Zeng, Negin Manshour, Farzaneh Esmaili, Biplab Poudel, Yuexu Jiang, Qing Shao, Jin Chen, Dong XuList of authors in order
- Landing page
-
https://doi.org/10.1002/advs.202404212Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1002/advs.202404212Direct OA link when available
- Concepts
-
Computer science, Sequence (biology), Embedding, Protein sequencing, Protein structure prediction, Artificial intelligence, Protein structure, Peptide sequence, Biology, Genetics, Gene, BiochemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
17Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 15, 2024: 2Per-year citation counts (last 5 years)
- References (count)
-
28Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4405330335 |
|---|---|
| doi | https://doi.org/10.1002/advs.202404212 |
| ids.doi | https://doi.org/10.1002/advs.202404212 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/39665266 |
| ids.openalex | https://openalex.org/W4405330335 |
| fwci | 8.16420283 |
| mesh[0].qualifier_ui | Q000737 |
| mesh[0].descriptor_ui | D011506 |
| mesh[0].is_major_topic | True |
| mesh[0].qualifier_name | chemistry |
| mesh[0].descriptor_name | Proteins |
| mesh[1].qualifier_ui | Q000378 |
| mesh[1].descriptor_ui | D011506 |
| mesh[1].is_major_topic | True |
| mesh[1].qualifier_name | metabolism |
| mesh[1].descriptor_name | Proteins |
| mesh[2].qualifier_ui | |
| mesh[2].descriptor_ui | D011487 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | |
| mesh[2].descriptor_name | Protein Conformation |
| mesh[3].qualifier_ui | |
| mesh[3].descriptor_ui | D000465 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | |
| mesh[3].descriptor_name | Algorithms |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D000069550 |
| mesh[4].is_major_topic | False |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Machine Learning |
| mesh[5].qualifier_ui | Q000737 |
| mesh[5].descriptor_ui | D011506 |
| mesh[5].is_major_topic | True |
| mesh[5].qualifier_name | chemistry |
| mesh[5].descriptor_name | Proteins |
| mesh[6].qualifier_ui | |
| mesh[6].descriptor_ui | D011487 |
| mesh[6].is_major_topic | False |
| mesh[6].qualifier_name | |
| mesh[6].descriptor_name | Protein Conformation |
| mesh[7].qualifier_ui | Q000379 |
| mesh[7].descriptor_ui | D019295 |
| mesh[7].is_major_topic | True |
| mesh[7].qualifier_name | methods |
| mesh[7].descriptor_name | Computational Biology |
| mesh[8].qualifier_ui | |
| mesh[8].descriptor_ui | D000069550 |
| mesh[8].is_major_topic | True |
| mesh[8].qualifier_name | |
| mesh[8].descriptor_name | Machine Learning |
| mesh[9].qualifier_ui | Q000737 |
| mesh[9].descriptor_ui | D011506 |
| mesh[9].is_major_topic | True |
| mesh[9].qualifier_name | chemistry |
| mesh[9].descriptor_name | Proteins |
| mesh[10].qualifier_ui | Q000378 |
| mesh[10].descriptor_ui | D011506 |
| mesh[10].is_major_topic | True |
| mesh[10].qualifier_name | metabolism |
| mesh[10].descriptor_name | Proteins |
| mesh[11].qualifier_ui | |
| mesh[11].descriptor_ui | D011487 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | |
| mesh[11].descriptor_name | Protein Conformation |
| mesh[12].qualifier_ui | |
| mesh[12].descriptor_ui | D000465 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | |
| mesh[12].descriptor_name | Algorithms |
| mesh[13].qualifier_ui | |
| mesh[13].descriptor_ui | D000069550 |
| mesh[13].is_major_topic | False |
| mesh[13].qualifier_name | |
| mesh[13].descriptor_name | Machine Learning |
| mesh[14].qualifier_ui | Q000737 |
| mesh[14].descriptor_ui | D011506 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | chemistry |
| mesh[14].descriptor_name | Proteins |
| mesh[15].qualifier_ui | Q000378 |
| mesh[15].descriptor_ui | D011506 |
| mesh[15].is_major_topic | True |
| mesh[15].qualifier_name | metabolism |
| mesh[15].descriptor_name | Proteins |
| mesh[16].qualifier_ui | |
| mesh[16].descriptor_ui | D011487 |
| mesh[16].is_major_topic | False |
| mesh[16].qualifier_name | |
| mesh[16].descriptor_name | Protein Conformation |
| mesh[17].qualifier_ui | |
| mesh[17].descriptor_ui | D000465 |
| mesh[17].is_major_topic | False |
| mesh[17].qualifier_name | |
| mesh[17].descriptor_name | Algorithms |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D000069550 |
| mesh[18].is_major_topic | False |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Machine Learning |
| type | article |
| title | S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure |
| awards[0].id | https://openalex.org/G2570542996 |
| awards[0].funder_id | https://openalex.org/F4320312143 |
| awards[0].display_name | |
| awards[0].funder_award_id | CIS230053 |
| awards[0].funder_display_name | National Centre for Supercomputing Applications |
| awards[1].id | https://openalex.org/G8027317136 |
| awards[1].funder_id | https://openalex.org/F4320332161 |
| awards[1].display_name | |
| awards[1].funder_award_id | R01LM014510 |
| awards[1].funder_display_name | National Institutes of Health |
| awards[2].id | https://openalex.org/G8064798875 |
| awards[2].funder_id | https://openalex.org/F4320306076 |
| awards[2].display_name | |
| awards[2].funder_award_id | #2138259 |
| awards[2].funder_display_name | National Science Foundation |
| awards[3].id | https://openalex.org/G2306305765 |
| awards[3].funder_id | https://openalex.org/F4320306080 |
| awards[3].display_name | |
| awards[3].funder_award_id | R35GM126985 |
| awards[3].funder_display_name | Foundation for the National Institutes of Health |
| biblio.issue | 5 |
| biblio.volume | 12 |
| biblio.last_page | e2404212 |
| biblio.first_page | e2404212 |
| 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 | 0.9995999932289124 |
| 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/T12254 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9995999932289124 |
| 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 | Machine Learning in Bioinformatics |
| topics[2].id | https://openalex.org/T10521 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9984999895095825 |
| topics[2].domain.id | https://openalex.org/domains/1 |
| topics[2].domain.display_name | Life Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/1312 |
| topics[2].subfield.display_name | Molecular Biology |
| topics[2].display_name | RNA and protein synthesis mechanisms |
| funders[0].id | https://openalex.org/F4320306076 |
| funders[0].ror | https://ror.org/021nxhr62 |
| funders[0].display_name | National Science Foundation |
| funders[1].id | https://openalex.org/F4320306080 |
| funders[1].ror | https://ror.org/00k86s890 |
| funders[1].display_name | Foundation for the National Institutes of Health |
| funders[2].id | https://openalex.org/F4320312143 |
| funders[2].ror | https://ror.org/03r10zj06 |
| funders[2].display_name | National Centre for Supercomputing Applications |
| funders[3].id | https://openalex.org/F4320332161 |
| funders[3].ror | https://ror.org/01cwqze88 |
| funders[3].display_name | National Institutes of Health |
| is_xpac | False |
| apc_list.value | 5000 |
| apc_list.currency | USD |
| apc_list.value_usd | 5000 |
| apc_paid.value | 5000 |
| apc_paid.currency | USD |
| apc_paid.value_usd | 5000 |
| concepts[0].id | https://openalex.org/C41008148 |
| concepts[0].level | 0 |
| concepts[0].score | 0.6640994548797607 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q21198 |
| concepts[0].display_name | Computer science |
| concepts[1].id | https://openalex.org/C2778112365 |
| concepts[1].level | 2 |
| concepts[1].score | 0.5896978974342346 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q3511065 |
| concepts[1].display_name | Sequence (biology) |
| concepts[2].id | https://openalex.org/C41608201 |
| concepts[2].level | 2 |
| concepts[2].score | 0.4684612452983856 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q980509 |
| concepts[2].display_name | Embedding |
| concepts[3].id | https://openalex.org/C10010492 |
| concepts[3].level | 4 |
| concepts[3].score | 0.4444971978664398 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q3142557 |
| concepts[3].display_name | Protein sequencing |
| concepts[4].id | https://openalex.org/C18051474 |
| concepts[4].level | 3 |
| concepts[4].score | 0.4231763482093811 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q899656 |
| concepts[4].display_name | Protein structure prediction |
| concepts[5].id | https://openalex.org/C154945302 |
| concepts[5].level | 1 |
| concepts[5].score | 0.418828547000885 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q11660 |
| concepts[5].display_name | Artificial intelligence |
| concepts[6].id | https://openalex.org/C47701112 |
| concepts[6].level | 2 |
| concepts[6].score | 0.3727740943431854 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q735188 |
| concepts[6].display_name | Protein structure |
| concepts[7].id | https://openalex.org/C167625842 |
| concepts[7].level | 3 |
| concepts[7].score | 0.20532655715942383 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q899763 |
| concepts[7].display_name | Peptide sequence |
| concepts[8].id | https://openalex.org/C86803240 |
| concepts[8].level | 0 |
| concepts[8].score | 0.1587936282157898 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[8].display_name | Biology |
| concepts[9].id | https://openalex.org/C54355233 |
| concepts[9].level | 1 |
| concepts[9].score | 0.0 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[9].display_name | Genetics |
| concepts[10].id | https://openalex.org/C104317684 |
| concepts[10].level | 2 |
| concepts[10].score | 0.0 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[10].display_name | Gene |
| concepts[11].id | https://openalex.org/C55493867 |
| concepts[11].level | 1 |
| concepts[11].score | 0.0 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q7094 |
| concepts[11].display_name | Biochemistry |
| keywords[0].id | https://openalex.org/keywords/computer-science |
| keywords[0].score | 0.6640994548797607 |
| keywords[0].display_name | Computer science |
| keywords[1].id | https://openalex.org/keywords/sequence |
| keywords[1].score | 0.5896978974342346 |
| keywords[1].display_name | Sequence (biology) |
| keywords[2].id | https://openalex.org/keywords/embedding |
| keywords[2].score | 0.4684612452983856 |
| keywords[2].display_name | Embedding |
| keywords[3].id | https://openalex.org/keywords/protein-sequencing |
| keywords[3].score | 0.4444971978664398 |
| keywords[3].display_name | Protein sequencing |
| keywords[4].id | https://openalex.org/keywords/protein-structure-prediction |
| keywords[4].score | 0.4231763482093811 |
| keywords[4].display_name | Protein structure prediction |
| keywords[5].id | https://openalex.org/keywords/artificial-intelligence |
| keywords[5].score | 0.418828547000885 |
| keywords[5].display_name | Artificial intelligence |
| keywords[6].id | https://openalex.org/keywords/protein-structure |
| keywords[6].score | 0.3727740943431854 |
| keywords[6].display_name | Protein structure |
| keywords[7].id | https://openalex.org/keywords/peptide-sequence |
| keywords[7].score | 0.20532655715942383 |
| keywords[7].display_name | Peptide sequence |
| keywords[8].id | https://openalex.org/keywords/biology |
| keywords[8].score | 0.1587936282157898 |
| keywords[8].display_name | Biology |
| language | en |
| locations[0].id | doi:10.1002/advs.202404212 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S2737737698 |
| locations[0].source.issn | 2198-3844 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | True |
| locations[0].source.issn_l | 2198-3844 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | True |
| locations[0].source.display_name | Advanced Science |
| locations[0].source.host_organization | https://openalex.org/P4310320595 |
| locations[0].source.host_organization_name | Wiley |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310320595 |
| locations[0].source.host_organization_lineage_names | Wiley |
| locations[0].license | cc-by |
| locations[0].pdf_url | |
| 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 | Advanced Science |
| locations[0].landing_page_url | https://doi.org/10.1002/advs.202404212 |
| locations[1].id | pmid:39665266 |
| 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 | Advanced science (Weinheim, Baden-Wurttemberg, Germany) |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/39665266 |
| locations[2].id | pmh:oai:doaj.org/article:101e1602d4e744c98022e6f97c2a8ae2 |
| locations[2].is_oa | False |
| locations[2].source.id | https://openalex.org/S4306401280 |
| 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 | DOAJ (DOAJ: Directory of Open Access Journals) |
| locations[2].source.host_organization | |
| locations[2].source.host_organization_name | |
| locations[2].license | |
| locations[2].pdf_url | |
| locations[2].version | submittedVersion |
| locations[2].raw_type | article |
| locations[2].license_id | |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | Advanced Science, Vol 12, Iss 5, Pp n/a-n/a (2025) |
| locations[2].landing_page_url | https://doaj.org/article/101e1602d4e744c98022e6f97c2a8ae2 |
| locations[3].id | pmh:oai:pubmedcentral.nih.gov:11791933 |
| locations[3].is_oa | True |
| locations[3].source.id | https://openalex.org/S2764455111 |
| locations[3].source.issn | |
| locations[3].source.type | repository |
| locations[3].source.is_oa | False |
| locations[3].source.issn_l | |
| locations[3].source.is_core | False |
| locations[3].source.is_in_doaj | False |
| locations[3].source.display_name | PubMed Central |
| locations[3].source.host_organization | https://openalex.org/I1299303238 |
| locations[3].source.host_organization_name | National Institutes of Health |
| locations[3].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[3].license | other-oa |
| locations[3].pdf_url | |
| locations[3].version | submittedVersion |
| locations[3].raw_type | Text |
| locations[3].license_id | https://openalex.org/licenses/other-oa |
| locations[3].is_accepted | False |
| locations[3].is_published | False |
| locations[3].raw_source_name | Adv Sci (Weinh) |
| locations[3].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/11791933 |
| indexed_in | crossref, doaj, pubmed |
| authorships[0].author.id | https://openalex.org/A5003943520 |
| authorships[0].author.orcid | https://orcid.org/0000-0003-1649-460X |
| authorships[0].author.display_name | Duolin Wang |
| authorships[0].countries | US |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[0].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[0].institutions[0].id | https://openalex.org/I76835614 |
| authorships[0].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[0].institutions[0].country_code | US |
| authorships[0].institutions[0].display_name | University of Missouri |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Duolin Wang |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[1].author.id | https://openalex.org/A5021973112 |
| authorships[1].author.orcid | https://orcid.org/0000-0003-4621-0372 |
| authorships[1].author.display_name | Mahdi Pourmirzaei |
| authorships[1].countries | US |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[1].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[1].institutions[0].id | https://openalex.org/I76835614 |
| authorships[1].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[1].institutions[0].country_code | US |
| authorships[1].institutions[0].display_name | University of Missouri |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Mahdi Pourmirzaei |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[2].author.id | https://openalex.org/A5039988690 |
| authorships[2].author.orcid | https://orcid.org/0000-0002-2752-4379 |
| authorships[2].author.display_name | Usman L. Abbas |
| authorships[2].countries | US |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I143302722 |
| authorships[2].affiliations[0].raw_affiliation_string | Chemical & Materials Engineering University of Kentucky Lexington KY 40506 USA |
| authorships[2].institutions[0].id | https://openalex.org/I143302722 |
| authorships[2].institutions[0].ror | https://ror.org/02k3smh20 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I143302722 |
| authorships[2].institutions[0].country_code | US |
| authorships[2].institutions[0].display_name | University of Kentucky |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Usman L. Abbas |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Chemical & Materials Engineering University of Kentucky Lexington KY 40506 USA |
| authorships[3].author.id | https://openalex.org/A5103082007 |
| authorships[3].author.orcid | https://orcid.org/0000-0001-7632-427X |
| authorships[3].author.display_name | Shuai Zeng |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[3].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[3].institutions[0].id | https://openalex.org/I76835614 |
| authorships[3].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | University of Missouri |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Shuai Zeng |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[4].author.id | https://openalex.org/A5047946195 |
| authorships[4].author.orcid | https://orcid.org/0009-0005-5552-6792 |
| authorships[4].author.display_name | Negin Manshour |
| authorships[4].countries | US |
| authorships[4].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[4].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[4].institutions[0].id | https://openalex.org/I76835614 |
| authorships[4].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[4].institutions[0].country_code | US |
| authorships[4].institutions[0].display_name | University of Missouri |
| authorships[4].author_position | middle |
| authorships[4].raw_author_name | Negin Manshour |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[5].author.id | https://openalex.org/A5076603704 |
| authorships[5].author.orcid | https://orcid.org/0000-0002-0002-7305 |
| authorships[5].author.display_name | Farzaneh Esmaili |
| authorships[5].countries | US |
| authorships[5].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[5].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[5].institutions[0].id | https://openalex.org/I76835614 |
| authorships[5].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[5].institutions[0].type | education |
| authorships[5].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[5].institutions[0].country_code | US |
| authorships[5].institutions[0].display_name | University of Missouri |
| authorships[5].author_position | middle |
| authorships[5].raw_author_name | Farzaneh Esmaili |
| authorships[5].is_corresponding | False |
| authorships[5].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[6].author.id | https://openalex.org/A5093382204 |
| authorships[6].author.orcid | |
| authorships[6].author.display_name | Biplab Poudel |
| authorships[6].countries | US |
| authorships[6].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[6].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[6].institutions[0].id | https://openalex.org/I76835614 |
| authorships[6].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[6].institutions[0].type | education |
| authorships[6].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[6].institutions[0].country_code | US |
| authorships[6].institutions[0].display_name | University of Missouri |
| authorships[6].author_position | middle |
| authorships[6].raw_author_name | Biplab Poudel |
| authorships[6].is_corresponding | False |
| authorships[6].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[7].author.id | https://openalex.org/A5112452050 |
| authorships[7].author.orcid | |
| authorships[7].author.display_name | Yuexu Jiang |
| authorships[7].countries | US |
| authorships[7].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[7].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[7].institutions[0].id | https://openalex.org/I76835614 |
| authorships[7].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[7].institutions[0].type | education |
| authorships[7].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[7].institutions[0].country_code | US |
| authorships[7].institutions[0].display_name | University of Missouri |
| authorships[7].author_position | middle |
| authorships[7].raw_author_name | Yuexu Jiang |
| authorships[7].is_corresponding | False |
| authorships[7].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[8].author.id | https://openalex.org/A5069728983 |
| authorships[8].author.orcid | https://orcid.org/0000-0001-9433-1131 |
| authorships[8].author.display_name | Qing Shao |
| authorships[8].countries | US |
| authorships[8].affiliations[0].institution_ids | https://openalex.org/I143302722 |
| authorships[8].affiliations[0].raw_affiliation_string | Chemical & Materials Engineering University of Kentucky Lexington KY 40506 USA |
| authorships[8].institutions[0].id | https://openalex.org/I143302722 |
| authorships[8].institutions[0].ror | https://ror.org/02k3smh20 |
| authorships[8].institutions[0].type | education |
| authorships[8].institutions[0].lineage | https://openalex.org/I143302722 |
| authorships[8].institutions[0].country_code | US |
| authorships[8].institutions[0].display_name | University of Kentucky |
| authorships[8].author_position | middle |
| authorships[8].raw_author_name | Qing Shao |
| authorships[8].is_corresponding | False |
| authorships[8].raw_affiliation_strings | Chemical & Materials Engineering University of Kentucky Lexington KY 40506 USA |
| authorships[9].author.id | https://openalex.org/A5100457144 |
| authorships[9].author.orcid | https://orcid.org/0000-0001-6076-1141 |
| authorships[9].author.display_name | Jin Chen |
| authorships[9].countries | US |
| authorships[9].affiliations[0].institution_ids | https://openalex.org/I32389192 |
| authorships[9].affiliations[0].raw_affiliation_string | Department of Medicine and Department of Biomedical Informatics and Data Science University of Alabama at Birmingham Birmingham AL 35294 USA |
| authorships[9].institutions[0].id | https://openalex.org/I32389192 |
| authorships[9].institutions[0].ror | https://ror.org/008s83205 |
| authorships[9].institutions[0].type | education |
| authorships[9].institutions[0].lineage | https://openalex.org/I32389192 |
| authorships[9].institutions[0].country_code | US |
| authorships[9].institutions[0].display_name | University of Alabama at Birmingham |
| authorships[9].author_position | middle |
| authorships[9].raw_author_name | Jin Chen |
| authorships[9].is_corresponding | False |
| authorships[9].raw_affiliation_strings | Department of Medicine and Department of Biomedical Informatics and Data Science University of Alabama at Birmingham Birmingham AL 35294 USA |
| authorships[10].author.id | https://openalex.org/A5082428303 |
| authorships[10].author.orcid | https://orcid.org/0000-0002-4809-0514 |
| authorships[10].author.display_name | Dong Xu |
| authorships[10].countries | US |
| authorships[10].affiliations[0].institution_ids | https://openalex.org/I76835614 |
| authorships[10].affiliations[0].raw_affiliation_string | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| authorships[10].institutions[0].id | https://openalex.org/I76835614 |
| authorships[10].institutions[0].ror | https://ror.org/02ymw8z06 |
| authorships[10].institutions[0].type | education |
| authorships[10].institutions[0].lineage | https://openalex.org/I76835614 |
| authorships[10].institutions[0].country_code | US |
| authorships[10].institutions[0].display_name | University of Missouri |
| authorships[10].author_position | last |
| authorships[10].raw_author_name | Dong Xu |
| authorships[10].is_corresponding | False |
| authorships[10].raw_affiliation_strings | Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center University of Missouri Columbia MO 65211 USA |
| has_content.pdf | False |
| has_content.grobid_xml | False |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://doi.org/10.1002/advs.202404212 |
| open_access.oa_status | gold |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | S‐PLM: Structure‐Aware Protein Language Model via Contrastive Learning Between Sequence and Structure |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-23T05:10:03.516525 |
| 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 | 0.9995999932289124 |
| 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/W2966686650, https://openalex.org/W2946599741, https://openalex.org/W2593264178, https://openalex.org/W3171039768, https://openalex.org/W2136856901, https://openalex.org/W2368468053, https://openalex.org/W2058542300, https://openalex.org/W2043066834, https://openalex.org/W2095784700, https://openalex.org/W4390971102 |
| cited_by_count | 17 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 15 |
| counts_by_year[1].year | 2024 |
| counts_by_year[1].cited_by_count | 2 |
| locations_count | 4 |
| best_oa_location.id | doi:10.1002/advs.202404212 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S2737737698 |
| best_oa_location.source.issn | 2198-3844 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | True |
| best_oa_location.source.issn_l | 2198-3844 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | True |
| best_oa_location.source.display_name | Advanced Science |
| best_oa_location.source.host_organization | https://openalex.org/P4310320595 |
| best_oa_location.source.host_organization_name | Wiley |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310320595 |
| best_oa_location.source.host_organization_lineage_names | Wiley |
| best_oa_location.license | cc-by |
| best_oa_location.pdf_url | |
| 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 | Advanced Science |
| best_oa_location.landing_page_url | https://doi.org/10.1002/advs.202404212 |
| primary_location.id | doi:10.1002/advs.202404212 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S2737737698 |
| primary_location.source.issn | 2198-3844 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | 2198-3844 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | True |
| primary_location.source.display_name | Advanced Science |
| primary_location.source.host_organization | https://openalex.org/P4310320595 |
| primary_location.source.host_organization_name | Wiley |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310320595 |
| primary_location.source.host_organization_lineage_names | Wiley |
| primary_location.license | cc-by |
| primary_location.pdf_url | |
| 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 | Advanced Science |
| primary_location.landing_page_url | https://doi.org/10.1002/advs.202404212 |
| publication_date | 2024-12-12 |
| publication_year | 2024 |
| referenced_works | https://openalex.org/W3144701084, https://openalex.org/W3177500196, https://openalex.org/W4327550249, https://openalex.org/W3146944767, https://openalex.org/W4288066876, https://openalex.org/W4362664122, https://openalex.org/W3166142427, https://openalex.org/W3177828909, https://openalex.org/W4205773061, https://openalex.org/W4365444089, https://openalex.org/W3108655343, https://openalex.org/W4362471278, https://openalex.org/W2788388592, https://openalex.org/W2604823638, https://openalex.org/W2120755421, https://openalex.org/W3106745904, https://openalex.org/W2085487226, https://openalex.org/W4382247824, https://openalex.org/W2054800842, https://openalex.org/W3011725683, https://openalex.org/W4210830887, https://openalex.org/W4220991280, https://openalex.org/W2194775991, https://openalex.org/W2889498145, https://openalex.org/W2041837226, https://openalex.org/W3164046276, https://openalex.org/W2950374603, https://openalex.org/W2104972430 |
| referenced_works_count | 28 |
| abstract_inverted_index.. | 191 |
| abstract_inverted_index.a | 91, 108, 111, 136 |
| abstract_inverted_index.3D | 61, 81, 92, 105 |
| abstract_inverted_index.To | 83 |
| abstract_inverted_index.an | 3 |
| abstract_inverted_index.as | 90 |
| abstract_inverted_index.at | 189 |
| abstract_inverted_index.by | 24 |
| abstract_inverted_index.in | 6, 64, 73, 110 |
| abstract_inverted_index.is | 88, 142 |
| abstract_inverted_index.it | 129 |
| abstract_inverted_index.of | 28, 34, 45, 59, 71, 107, 138 |
| abstract_inverted_index.on | 48, 80, 118, 162 |
| abstract_inverted_index.to | 20, 100, 122, 144, 172 |
| abstract_inverted_index.PLM | 94 |
| abstract_inverted_index.The | 40, 153 |
| abstract_inverted_index.all | 163 |
| abstract_inverted_index.and | 9, 31, 42, 104, 127, 166, 178, 182 |
| abstract_inverted_index.are | 187 |
| abstract_inverted_index.for | 147 |
| abstract_inverted_index.its | 183 |
| abstract_inverted_index.the | 26, 32, 37, 49, 53, 57, 68, 102, 124 |
| abstract_inverted_index.PLMs | 46, 66, 72, 161 |
| abstract_inverted_index.both | 176 |
| abstract_inverted_index.from | 52, 133 |
| abstract_inverted_index.into | 130 |
| abstract_inverted_index.lack | 58 |
| abstract_inverted_index.most | 65 |
| abstract_inverted_index.over | 159 |
| abstract_inverted_index.play | 2 |
| abstract_inverted_index.role | 5 |
| abstract_inverted_index.that | 95 |
| abstract_inverted_index.this | 85 |
| abstract_inverted_index.with | 36 |
| abstract_inverted_index.ESM2. | 134 |
| abstract_inverted_index.Large | 12 |
| abstract_inverted_index.adapt | 145 |
| abstract_inverted_index.align | 101 |
| abstract_inverted_index.embed | 123 |
| abstract_inverted_index.fuses | 128 |
| abstract_inverted_index.those | 77 |
| abstract_inverted_index.tools | 141, 186 |
| abstract_inverted_index.(PLMs) | 16 |
| abstract_inverted_index.design | 33, 43 |
| abstract_inverted_index.gained | 51 |
| abstract_inverted_index.issue, | 86 |
| abstract_inverted_index.latent | 113 |
| abstract_inverted_index.models | 15 |
| abstract_inverted_index.relies | 47 |
| abstract_inverted_index.space. | 114 |
| abstract_inverted_index.tasks, | 168 |
| abstract_inverted_index.tasks. | 152 |
| abstract_inverted_index.tuning | 140, 185 |
| abstract_inverted_index.S‐PLM | 87, 115, 146, 181 |
| abstract_inverted_index.address | 84 |
| abstract_inverted_index.applies | 116 |
| abstract_inverted_index.crucial | 60 |
| abstract_inverted_index.desired | 38 |
| abstract_inverted_index.diverse | 148 |
| abstract_inverted_index.heavily | 78 |
| abstract_inverted_index.inputs. | 180 |
| abstract_inverted_index.library | 137 |
| abstract_inverted_index.methods | 174 |
| abstract_inverted_index.present | 17 |
| abstract_inverted_index.protein | 13, 22, 29, 54, 109, 120, 150, 164 |
| abstract_inverted_index.reshape | 21 |
| abstract_inverted_index.results | 154 |
| abstract_inverted_index.various | 7, 74 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.However, | 56 |
| abstract_inverted_index.Proteins | 1 |
| abstract_inverted_index.capacity | 44, 70 |
| abstract_inverted_index.language | 14 |
| abstract_inverted_index.learning | 99 |
| abstract_inverted_index.proteins | 35 |
| abstract_inverted_index.provided | 143 |
| abstract_inverted_index.research | 23 |
| abstract_inverted_index.sequence | 103, 177 |
| abstract_inverted_index.superior | 157 |
| abstract_inverted_index.utilizes | 96 |
| abstract_inverted_index.S‐PLM's | 156 |
| abstract_inverted_index.achieving | 169 |
| abstract_inverted_index.available | 188 |
| abstract_inverted_index.dependent | 79 |
| abstract_inverted_index.embedding | 132 |
| abstract_inverted_index.essential | 4 |
| abstract_inverted_index.excellent | 18 |
| abstract_inverted_index.functions | 30 |
| abstract_inverted_index.potential | 19 |
| abstract_inverted_index.requiring | 175 |
| abstract_inverted_index.restricts | 67 |
| abstract_inverted_index.structure | 62, 106, 179 |
| abstract_inverted_index.biological | 8 |
| abstract_inverted_index.clustering | 165 |
| abstract_inverted_index.comparable | 171 |
| abstract_inverted_index.downstream | 149 |
| abstract_inverted_index.especially | 76 |
| abstract_inverted_index.functions. | 39 |
| abstract_inverted_index.introduced | 89 |
| abstract_inverted_index.prediction | 41, 69, 151 |
| abstract_inverted_index.processes. | 11 |
| abstract_inverted_index.sequences. | 55 |
| abstract_inverted_index.structural | 125 |
| abstract_inverted_index.structures | 121 |
| abstract_inverted_index.contrastive | 98 |
| abstract_inverted_index.coordinated | 112 |
| abstract_inverted_index.demonstrate | 155 |
| abstract_inverted_index.engineering | 10 |
| abstract_inverted_index.information | 63, 126 |
| abstract_inverted_index.lightweight | 139, 184 |
| abstract_inverted_index.performance | 158 |
| abstract_inverted_index.structures. | 82 |
| abstract_inverted_index.accelerating | 25 |
| abstract_inverted_index.multi‐view | 97 |
| abstract_inverted_index.Additionally, | 135 |
| abstract_inverted_index.applications, | 75 |
| abstract_inverted_index.determination | 27 |
| abstract_inverted_index.classification | 167 |
| abstract_inverted_index.representation | 50 |
| abstract_inverted_index.competitiveness | 170 |
| abstract_inverted_index.sequence‐only | 160 |
| abstract_inverted_index.sequence‐based | 131 |
| abstract_inverted_index.structure‐aware | 93 |
| abstract_inverted_index.Swin‐Transformer | 117 |
| abstract_inverted_index.AlphaFold‐predicted | 119 |
| abstract_inverted_index.state‐of‐the‐art | 173 |
| abstract_inverted_index.https://github.com/duolinwang/S-PLM/ | 190 |
| cited_by_percentile_year.max | 100 |
| cited_by_percentile_year.min | 94 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 11 |
| citation_normalized_percentile.value | 0.96655107 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |