Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants Article Swipe
Nikita R. Dsouza
,
Neshatul Haque
,
Swarnendu Tripathi
,
Michael T. Zimmermann
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/ijms252212018
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3390/ijms252212018
Clinical genomics sequencing is rapidly expanding the number of variants that need to be functionally elucidated. Interpreting genetic variants (i.e., mutations) usually begins by identifying how they affect protein-coding sequences. Still, the three-dimensional (3D) protein molecule is rarely considered for large-scale variant analysis, nor in analyses of how proteins interact with each other and their environment. We propose a standardized approach to scoring protein surface property changes as a new dimension for functionally and mechanistically interpreting genomic variants. Further, it directs hypothesis generation for functional genomics research to learn more about the encoded protein’s function. We developed a novel method leveraging 3D structures and time-dependent simulations to score and statistically evaluate protein surface property changes. We evaluated positive controls composed of eight thermophilic versus mesophilic orthologs and variants that experimentally change the protein’s solubility, which all showed large and statistically significant differences in charge distribution (p < 0.01). We scored static 3D structures and dynamic ensembles for 43 independent variants (23 pathogenic and 20 uninterpreted) across four proteins. Focusing on the potassium ion channel, KCNK9, the average local surface potential shifts were 0.41 kBT/ec with an average p-value of 1 × 10−2. In contrast, dynamic ensemble shifts averaged 1.15 kBT/ec with an average p-value of 1 × 10−5, enabling the identification of changes far from mutated sites. This study demonstrates that an objective assessment of how mutations affect electrostatic distributions of protein surfaces can aid in interpreting genomic variants discovered through clinical genomic sequencing.
Related Topics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/ijms252212018
- OA Status
- gold
- Cited By
- 1
- References
- 48
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4404189058
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4404189058Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3390/ijms252212018Digital Object Identifier
- Title
-
Assessing Protein Surface-Based Scoring for Interpreting Genomic VariantsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-11-08Full publication date if available
- Authors
-
Nikita R. Dsouza, Neshatul Haque, Swarnendu Tripathi, Michael T. ZimmermannList of authors in order
- Landing page
-
https://doi.org/10.3390/ijms252212018Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.3390/ijms252212018Direct OA link when available
- Concepts
-
Computational biology, Surface protein, Biology, Genetics, Bioinformatics, VirologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
1Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1Per-year citation counts (last 5 years)
- References (count)
-
48Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4404189058 |
|---|---|
| doi | https://doi.org/10.3390/ijms252212018 |
| ids.doi | https://doi.org/10.3390/ijms252212018 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/39596086 |
| ids.openalex | https://openalex.org/W4404189058 |
| fwci | 0.48024723 |
| mesh[0].qualifier_ui | |
| mesh[0].descriptor_ui | D006801 |
| mesh[0].is_major_topic | False |
| mesh[0].qualifier_name | |
| mesh[0].descriptor_name | Humans |
| mesh[1].qualifier_ui | Q000379 |
| mesh[1].descriptor_ui | D023281 |
| mesh[1].is_major_topic | True |
| mesh[1].qualifier_name | methods |
| mesh[1].descriptor_name | Genomics |
| mesh[2].qualifier_ui | |
| mesh[2].descriptor_ui | D014644 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | |
| mesh[2].descriptor_name | Genetic Variation |
| mesh[3].qualifier_ui | |
| mesh[3].descriptor_ui | D011487 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | |
| mesh[3].descriptor_name | Protein Conformation |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D009154 |
| mesh[4].is_major_topic | False |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Mutation |
| mesh[5].qualifier_ui | Q000235 |
| mesh[5].descriptor_ui | D011506 |
| mesh[5].is_major_topic | False |
| mesh[5].qualifier_name | genetics |
| mesh[5].descriptor_name | Proteins |
| mesh[6].qualifier_ui | Q000737 |
| mesh[6].descriptor_ui | D011506 |
| mesh[6].is_major_topic | False |
| mesh[6].qualifier_name | chemistry |
| mesh[6].descriptor_name | Proteins |
| mesh[7].qualifier_ui | Q000378 |
| mesh[7].descriptor_ui | D011506 |
| mesh[7].is_major_topic | False |
| mesh[7].qualifier_name | metabolism |
| mesh[7].descriptor_name | Proteins |
| mesh[8].qualifier_ui | |
| mesh[8].descriptor_ui | D008958 |
| mesh[8].is_major_topic | False |
| mesh[8].qualifier_name | |
| mesh[8].descriptor_name | Models, Molecular |
| mesh[9].qualifier_ui | |
| mesh[9].descriptor_ui | D013499 |
| mesh[9].is_major_topic | False |
| mesh[9].qualifier_name | |
| mesh[9].descriptor_name | Surface Properties |
| mesh[10].qualifier_ui | |
| mesh[10].descriptor_ui | D006801 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | |
| mesh[10].descriptor_name | Humans |
| mesh[11].qualifier_ui | Q000379 |
| mesh[11].descriptor_ui | D023281 |
| mesh[11].is_major_topic | True |
| mesh[11].qualifier_name | methods |
| mesh[11].descriptor_name | Genomics |
| mesh[12].qualifier_ui | |
| mesh[12].descriptor_ui | D014644 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | |
| mesh[12].descriptor_name | Genetic Variation |
| mesh[13].qualifier_ui | |
| mesh[13].descriptor_ui | D011487 |
| mesh[13].is_major_topic | False |
| mesh[13].qualifier_name | |
| mesh[13].descriptor_name | Protein Conformation |
| mesh[14].qualifier_ui | |
| mesh[14].descriptor_ui | D009154 |
| mesh[14].is_major_topic | False |
| mesh[14].qualifier_name | |
| mesh[14].descriptor_name | Mutation |
| mesh[15].qualifier_ui | Q000235 |
| mesh[15].descriptor_ui | D011506 |
| mesh[15].is_major_topic | False |
| mesh[15].qualifier_name | genetics |
| mesh[15].descriptor_name | Proteins |
| mesh[16].qualifier_ui | Q000737 |
| mesh[16].descriptor_ui | D011506 |
| mesh[16].is_major_topic | False |
| mesh[16].qualifier_name | chemistry |
| mesh[16].descriptor_name | Proteins |
| mesh[17].qualifier_ui | Q000378 |
| mesh[17].descriptor_ui | D011506 |
| mesh[17].is_major_topic | False |
| mesh[17].qualifier_name | metabolism |
| mesh[17].descriptor_name | Proteins |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D008958 |
| mesh[18].is_major_topic | False |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Models, Molecular |
| mesh[19].qualifier_ui | |
| mesh[19].descriptor_ui | D013499 |
| mesh[19].is_major_topic | False |
| mesh[19].qualifier_name | |
| mesh[19].descriptor_name | Surface Properties |
| mesh[20].qualifier_ui | |
| mesh[20].descriptor_ui | D006801 |
| mesh[20].is_major_topic | False |
| mesh[20].qualifier_name | |
| mesh[20].descriptor_name | Humans |
| mesh[21].qualifier_ui | Q000379 |
| mesh[21].descriptor_ui | D023281 |
| mesh[21].is_major_topic | True |
| mesh[21].qualifier_name | methods |
| mesh[21].descriptor_name | Genomics |
| mesh[22].qualifier_ui | |
| mesh[22].descriptor_ui | D014644 |
| mesh[22].is_major_topic | False |
| mesh[22].qualifier_name | |
| mesh[22].descriptor_name | Genetic Variation |
| mesh[23].qualifier_ui | |
| mesh[23].descriptor_ui | D011487 |
| mesh[23].is_major_topic | False |
| mesh[23].qualifier_name | |
| mesh[23].descriptor_name | Protein Conformation |
| mesh[24].qualifier_ui | |
| mesh[24].descriptor_ui | D009154 |
| mesh[24].is_major_topic | False |
| mesh[24].qualifier_name | |
| mesh[24].descriptor_name | Mutation |
| mesh[25].qualifier_ui | Q000235 |
| mesh[25].descriptor_ui | D011506 |
| mesh[25].is_major_topic | False |
| mesh[25].qualifier_name | genetics |
| mesh[25].descriptor_name | Proteins |
| mesh[26].qualifier_ui | Q000737 |
| mesh[26].descriptor_ui | D011506 |
| mesh[26].is_major_topic | False |
| mesh[26].qualifier_name | chemistry |
| mesh[26].descriptor_name | Proteins |
| mesh[27].qualifier_ui | Q000378 |
| mesh[27].descriptor_ui | D011506 |
| mesh[27].is_major_topic | False |
| mesh[27].qualifier_name | metabolism |
| mesh[27].descriptor_name | Proteins |
| mesh[28].qualifier_ui | |
| mesh[28].descriptor_ui | D008958 |
| mesh[28].is_major_topic | False |
| mesh[28].qualifier_name | |
| mesh[28].descriptor_name | Models, Molecular |
| mesh[29].qualifier_ui | |
| mesh[29].descriptor_ui | D013499 |
| mesh[29].is_major_topic | False |
| mesh[29].qualifier_name | |
| mesh[29].descriptor_name | Surface Properties |
| mesh[30].qualifier_ui | |
| mesh[30].descriptor_ui | D006801 |
| mesh[30].is_major_topic | False |
| mesh[30].qualifier_name | |
| mesh[30].descriptor_name | Humans |
| mesh[31].qualifier_ui | Q000379 |
| mesh[31].descriptor_ui | D023281 |
| mesh[31].is_major_topic | True |
| mesh[31].qualifier_name | methods |
| mesh[31].descriptor_name | Genomics |
| mesh[32].qualifier_ui | |
| mesh[32].descriptor_ui | D014644 |
| mesh[32].is_major_topic | False |
| mesh[32].qualifier_name | |
| mesh[32].descriptor_name | Genetic Variation |
| mesh[33].qualifier_ui | |
| mesh[33].descriptor_ui | D011487 |
| mesh[33].is_major_topic | False |
| mesh[33].qualifier_name | |
| mesh[33].descriptor_name | Protein Conformation |
| mesh[34].qualifier_ui | |
| mesh[34].descriptor_ui | D009154 |
| mesh[34].is_major_topic | False |
| mesh[34].qualifier_name | |
| mesh[34].descriptor_name | Mutation |
| mesh[35].qualifier_ui | Q000235 |
| mesh[35].descriptor_ui | D011506 |
| mesh[35].is_major_topic | False |
| mesh[35].qualifier_name | genetics |
| mesh[35].descriptor_name | Proteins |
| mesh[36].qualifier_ui | Q000737 |
| mesh[36].descriptor_ui | D011506 |
| mesh[36].is_major_topic | False |
| mesh[36].qualifier_name | chemistry |
| mesh[36].descriptor_name | Proteins |
| mesh[37].qualifier_ui | Q000378 |
| mesh[37].descriptor_ui | D011506 |
| mesh[37].is_major_topic | False |
| mesh[37].qualifier_name | metabolism |
| mesh[37].descriptor_name | Proteins |
| mesh[38].qualifier_ui | |
| mesh[38].descriptor_ui | D008958 |
| mesh[38].is_major_topic | False |
| mesh[38].qualifier_name | |
| mesh[38].descriptor_name | Models, Molecular |
| mesh[39].qualifier_ui | |
| mesh[39].descriptor_ui | D013499 |
| mesh[39].is_major_topic | False |
| mesh[39].qualifier_name | |
| mesh[39].descriptor_name | Surface Properties |
| type | article |
| title | Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants |
| biblio.issue | 22 |
| biblio.volume | 25 |
| biblio.last_page | 12018 |
| biblio.first_page | 12018 |
| topics[0].id | https://openalex.org/T10521 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 0.9991999864578247 |
| 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 | RNA and protein synthesis mechanisms |
| 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 | 0.9883999824523926 |
| 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/T10044 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9836999773979187 |
| 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 | Protein Structure and Dynamics |
| is_xpac | False |
| apc_list.value | 2300 |
| apc_list.currency | CHF |
| apc_list.value_usd | 2490 |
| apc_paid.value | 2300 |
| apc_paid.currency | CHF |
| apc_paid.value_usd | 2490 |
| concepts[0].id | https://openalex.org/C70721500 |
| concepts[0].level | 1 |
| concepts[0].score | 0.6199421286582947 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[0].display_name | Computational biology |
| concepts[1].id | https://openalex.org/C3019232848 |
| concepts[1].level | 2 |
| concepts[1].score | 0.47658488154411316 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q29548 |
| concepts[1].display_name | Surface protein |
| concepts[2].id | https://openalex.org/C86803240 |
| concepts[2].level | 0 |
| concepts[2].score | 0.40273457765579224 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[2].display_name | Biology |
| concepts[3].id | https://openalex.org/C54355233 |
| concepts[3].level | 1 |
| concepts[3].score | 0.37018316984176636 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[3].display_name | Genetics |
| concepts[4].id | https://openalex.org/C60644358 |
| concepts[4].level | 1 |
| concepts[4].score | 0.34170567989349365 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q128570 |
| concepts[4].display_name | Bioinformatics |
| concepts[5].id | https://openalex.org/C159047783 |
| concepts[5].level | 1 |
| concepts[5].score | 0.0 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q7215 |
| concepts[5].display_name | Virology |
| keywords[0].id | https://openalex.org/keywords/computational-biology |
| keywords[0].score | 0.6199421286582947 |
| keywords[0].display_name | Computational biology |
| keywords[1].id | https://openalex.org/keywords/surface-protein |
| keywords[1].score | 0.47658488154411316 |
| keywords[1].display_name | Surface protein |
| keywords[2].id | https://openalex.org/keywords/biology |
| keywords[2].score | 0.40273457765579224 |
| keywords[2].display_name | Biology |
| keywords[3].id | https://openalex.org/keywords/genetics |
| keywords[3].score | 0.37018316984176636 |
| keywords[3].display_name | Genetics |
| keywords[4].id | https://openalex.org/keywords/bioinformatics |
| keywords[4].score | 0.34170567989349365 |
| keywords[4].display_name | Bioinformatics |
| language | en |
| locations[0].id | doi:10.3390/ijms252212018 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S10623703 |
| locations[0].source.issn | 1422-0067, 1661-6596 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | True |
| locations[0].source.issn_l | 1422-0067 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | False |
| locations[0].source.display_name | International Journal of Molecular Sciences |
| locations[0].source.host_organization | https://openalex.org/P4310310987 |
| locations[0].source.host_organization_name | Multidisciplinary Digital Publishing Institute |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310310987 |
| locations[0].source.host_organization_lineage_names | Multidisciplinary Digital Publishing Institute |
| 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 | International Journal of Molecular Sciences |
| locations[0].landing_page_url | https://doi.org/10.3390/ijms252212018 |
| locations[1].id | pmid:39596086 |
| 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 | International journal of molecular sciences |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/39596086 |
| locations[2].id | pmh:oai:pubmedcentral.nih.gov:11594063 |
| 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 | Int J Mol Sci |
| locations[2].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/11594063 |
| indexed_in | crossref, pubmed |
| authorships[0].author.id | https://openalex.org/A5001517067 |
| authorships[0].author.orcid | |
| authorships[0].author.display_name | Nikita R. Dsouza |
| authorships[0].countries | US |
| authorships[0].affiliations[0].institution_ids | https://openalex.org/I204308271 |
| authorships[0].affiliations[0].raw_affiliation_string | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[0].institutions[0].id | https://openalex.org/I204308271 |
| authorships[0].institutions[0].ror | https://ror.org/00qqv6244 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I204308271 |
| authorships[0].institutions[0].country_code | US |
| authorships[0].institutions[0].display_name | Medical College of Wisconsin |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Nikita R. Dsouza |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[1].author.id | https://openalex.org/A5021733365 |
| authorships[1].author.orcid | https://orcid.org/0000-0001-7494-6059 |
| authorships[1].author.display_name | Neshatul Haque |
| authorships[1].countries | US |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I204308271 |
| authorships[1].affiliations[0].raw_affiliation_string | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[1].institutions[0].id | https://openalex.org/I204308271 |
| authorships[1].institutions[0].ror | https://ror.org/00qqv6244 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I204308271 |
| authorships[1].institutions[0].country_code | US |
| authorships[1].institutions[0].display_name | Medical College of Wisconsin |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Neshatul Haque |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[2].author.id | https://openalex.org/A5046973392 |
| authorships[2].author.orcid | |
| authorships[2].author.display_name | Swarnendu Tripathi |
| authorships[2].countries | US |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I204308271 |
| authorships[2].affiliations[0].raw_affiliation_string | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[2].institutions[0].id | https://openalex.org/I204308271 |
| authorships[2].institutions[0].ror | https://ror.org/00qqv6244 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I204308271 |
| authorships[2].institutions[0].country_code | US |
| authorships[2].institutions[0].display_name | Medical College of Wisconsin |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Swarnendu Tripathi |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[3].author.id | https://openalex.org/A5054127002 |
| authorships[3].author.orcid | https://orcid.org/0000-0001-7073-0525 |
| authorships[3].author.display_name | Michael T. Zimmermann |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I204308271 |
| authorships[3].affiliations[0].raw_affiliation_string | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[3].affiliations[1].institution_ids | https://openalex.org/I204308271 |
| authorships[3].affiliations[1].raw_affiliation_string | Data Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[3].affiliations[2].institution_ids | https://openalex.org/I204308271 |
| authorships[3].affiliations[2].raw_affiliation_string | Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA |
| authorships[3].institutions[0].id | https://openalex.org/I204308271 |
| authorships[3].institutions[0].ror | https://ror.org/00qqv6244 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I204308271 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | Medical College of Wisconsin |
| authorships[3].author_position | last |
| authorships[3].raw_author_name | Michael T. Zimmermann |
| authorships[3].is_corresponding | True |
| authorships[3].raw_affiliation_strings | Computational Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomics Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA, Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, 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/10.3390/ijms252212018 |
| open_access.oa_status | gold |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T10521 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 0.9991999864578247 |
| 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 | RNA and protein synthesis mechanisms |
| related_works | https://openalex.org/W4391375266, https://openalex.org/W2082860237, https://openalex.org/W2119695867, https://openalex.org/W2130076355, https://openalex.org/W1990804418, https://openalex.org/W1993764875, https://openalex.org/W2046158694, https://openalex.org/W2788277189, https://openalex.org/W2013243191, https://openalex.org/W1837502840 |
| cited_by_count | 1 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 1 |
| locations_count | 3 |
| best_oa_location.id | doi:10.3390/ijms252212018 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S10623703 |
| best_oa_location.source.issn | 1422-0067, 1661-6596 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | True |
| best_oa_location.source.issn_l | 1422-0067 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | False |
| best_oa_location.source.display_name | International Journal of Molecular Sciences |
| best_oa_location.source.host_organization | https://openalex.org/P4310310987 |
| best_oa_location.source.host_organization_name | Multidisciplinary Digital Publishing Institute |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310310987 |
| best_oa_location.source.host_organization_lineage_names | Multidisciplinary Digital Publishing Institute |
| 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 | International Journal of Molecular Sciences |
| best_oa_location.landing_page_url | https://doi.org/10.3390/ijms252212018 |
| primary_location.id | doi:10.3390/ijms252212018 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S10623703 |
| primary_location.source.issn | 1422-0067, 1661-6596 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | 1422-0067 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | False |
| primary_location.source.display_name | International Journal of Molecular Sciences |
| primary_location.source.host_organization | https://openalex.org/P4310310987 |
| primary_location.source.host_organization_name | Multidisciplinary Digital Publishing Institute |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310310987 |
| primary_location.source.host_organization_lineage_names | Multidisciplinary Digital Publishing Institute |
| 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 | International Journal of Molecular Sciences |
| primary_location.landing_page_url | https://doi.org/10.3390/ijms252212018 |
| publication_date | 2024-11-08 |
| publication_year | 2024 |
| referenced_works | https://openalex.org/W2906311950, https://openalex.org/W2905810301, https://openalex.org/W2897067527, https://openalex.org/W2959541742, https://openalex.org/W2781194065, https://openalex.org/W2051978340, https://openalex.org/W6745057384, https://openalex.org/W1975328482, https://openalex.org/W2097455735, https://openalex.org/W3029661147, https://openalex.org/W2170547473, https://openalex.org/W1946582282, https://openalex.org/W2155091686, https://openalex.org/W2031215084, https://openalex.org/W6628682427, https://openalex.org/W3039382149, https://openalex.org/W3177828909, https://openalex.org/W4388602745, https://openalex.org/W4282546381, https://openalex.org/W3165101377, https://openalex.org/W2116121073, https://openalex.org/W2158116492, https://openalex.org/W2154866190, https://openalex.org/W6629658836, https://openalex.org/W4281490686, https://openalex.org/W2130479394, https://openalex.org/W2978810318, https://openalex.org/W2406171343, https://openalex.org/W2149525061, https://openalex.org/W2155201844, https://openalex.org/W2032443344, https://openalex.org/W2041345208, https://openalex.org/W2410869890, https://openalex.org/W2023490488, https://openalex.org/W2150981663, https://openalex.org/W2109154308, https://openalex.org/W2587567366, https://openalex.org/W2854827211, https://openalex.org/W2206954826, https://openalex.org/W2132262459, https://openalex.org/W1470759511, https://openalex.org/W2052083266, https://openalex.org/W2731784911, https://openalex.org/W2165565773, https://openalex.org/W2047399603, https://openalex.org/W1494567425, https://openalex.org/W3125756628, https://openalex.org/W2951279857 |
| referenced_works_count | 48 |
| abstract_inverted_index.1 | 189, 205 |
| abstract_inverted_index.a | 58, 68, 97 |
| abstract_inverted_index.(p | 145 |
| abstract_inverted_index.20 | 163 |
| abstract_inverted_index.3D | 101, 151 |
| abstract_inverted_index.43 | 157 |
| abstract_inverted_index.In | 192 |
| abstract_inverted_index.We | 56, 95, 115, 148 |
| abstract_inverted_index.an | 185, 201, 221 |
| abstract_inverted_index.as | 67 |
| abstract_inverted_index.be | 13 |
| abstract_inverted_index.by | 23 |
| abstract_inverted_index.in | 44, 142, 235 |
| abstract_inverted_index.is | 3, 36 |
| abstract_inverted_index.it | 79 |
| abstract_inverted_index.of | 8, 46, 120, 188, 204, 211, 224, 230 |
| abstract_inverted_index.on | 169 |
| abstract_inverted_index.to | 12, 61, 87, 106 |
| abstract_inverted_index.× | 190, 206 |
| abstract_inverted_index.(23 | 160 |
| abstract_inverted_index.aid | 234 |
| abstract_inverted_index.all | 135 |
| abstract_inverted_index.and | 53, 73, 103, 108, 126, 138, 153, 162 |
| abstract_inverted_index.can | 233 |
| abstract_inverted_index.far | 213 |
| abstract_inverted_index.for | 39, 71, 83, 156 |
| abstract_inverted_index.how | 25, 47, 225 |
| abstract_inverted_index.ion | 172 |
| abstract_inverted_index.new | 69 |
| abstract_inverted_index.nor | 43 |
| abstract_inverted_index.the | 6, 31, 91, 131, 170, 175, 209 |
| abstract_inverted_index.< | 146 |
| abstract_inverted_index.(3D) | 33 |
| abstract_inverted_index.0.41 | 182 |
| abstract_inverted_index.1.15 | 198 |
| abstract_inverted_index.This | 217 |
| abstract_inverted_index.each | 51 |
| abstract_inverted_index.four | 166 |
| abstract_inverted_index.from | 214 |
| abstract_inverted_index.more | 89 |
| abstract_inverted_index.need | 11 |
| abstract_inverted_index.that | 10, 128, 220 |
| abstract_inverted_index.they | 26 |
| abstract_inverted_index.were | 181 |
| abstract_inverted_index.with | 50, 184, 200 |
| abstract_inverted_index.about | 90 |
| abstract_inverted_index.eight | 121 |
| abstract_inverted_index.large | 137 |
| abstract_inverted_index.learn | 88 |
| abstract_inverted_index.local | 177 |
| abstract_inverted_index.novel | 98 |
| abstract_inverted_index.other | 52 |
| abstract_inverted_index.score | 107 |
| abstract_inverted_index.study | 218 |
| abstract_inverted_index.their | 54 |
| abstract_inverted_index.which | 134 |
| abstract_inverted_index.(i.e., | 19 |
| abstract_inverted_index.0.01). | 147 |
| abstract_inverted_index.KCNK9, | 174 |
| abstract_inverted_index.Still, | 30 |
| abstract_inverted_index.across | 165 |
| abstract_inverted_index.affect | 27, 227 |
| abstract_inverted_index.begins | 22 |
| abstract_inverted_index.change | 130 |
| abstract_inverted_index.charge | 143 |
| abstract_inverted_index.kBT/ec | 183, 199 |
| abstract_inverted_index.method | 99 |
| abstract_inverted_index.number | 7 |
| abstract_inverted_index.rarely | 37 |
| abstract_inverted_index.scored | 149 |
| abstract_inverted_index.shifts | 180, 196 |
| abstract_inverted_index.showed | 136 |
| abstract_inverted_index.sites. | 216 |
| abstract_inverted_index.static | 150 |
| abstract_inverted_index.versus | 123 |
| abstract_inverted_index.10−2. | 191 |
| abstract_inverted_index.10−5, | 207 |
| abstract_inverted_index.average | 176, 186, 202 |
| abstract_inverted_index.changes | 66, 212 |
| abstract_inverted_index.directs | 80 |
| abstract_inverted_index.dynamic | 154, 194 |
| abstract_inverted_index.encoded | 92 |
| abstract_inverted_index.genetic | 17 |
| abstract_inverted_index.genomic | 76, 237, 242 |
| abstract_inverted_index.mutated | 215 |
| abstract_inverted_index.p-value | 187, 203 |
| abstract_inverted_index.propose | 57 |
| abstract_inverted_index.protein | 34, 63, 111, 231 |
| abstract_inverted_index.rapidly | 4 |
| abstract_inverted_index.scoring | 62 |
| abstract_inverted_index.surface | 64, 112, 178 |
| abstract_inverted_index.through | 240 |
| abstract_inverted_index.usually | 21 |
| abstract_inverted_index.variant | 41 |
| abstract_inverted_index.Clinical | 0 |
| abstract_inverted_index.Focusing | 168 |
| abstract_inverted_index.Further, | 78 |
| abstract_inverted_index.analyses | 45 |
| abstract_inverted_index.approach | 60 |
| abstract_inverted_index.averaged | 197 |
| abstract_inverted_index.changes. | 114 |
| abstract_inverted_index.channel, | 173 |
| abstract_inverted_index.clinical | 241 |
| abstract_inverted_index.composed | 119 |
| abstract_inverted_index.controls | 118 |
| abstract_inverted_index.enabling | 208 |
| abstract_inverted_index.ensemble | 195 |
| abstract_inverted_index.evaluate | 110 |
| abstract_inverted_index.genomics | 1, 85 |
| abstract_inverted_index.interact | 49 |
| abstract_inverted_index.molecule | 35 |
| abstract_inverted_index.positive | 117 |
| abstract_inverted_index.property | 65, 113 |
| abstract_inverted_index.proteins | 48 |
| abstract_inverted_index.research | 86 |
| abstract_inverted_index.surfaces | 232 |
| abstract_inverted_index.variants | 9, 18, 127, 159, 238 |
| abstract_inverted_index.analysis, | 42 |
| abstract_inverted_index.contrast, | 193 |
| abstract_inverted_index.developed | 96 |
| abstract_inverted_index.dimension | 70 |
| abstract_inverted_index.ensembles | 155 |
| abstract_inverted_index.evaluated | 116 |
| abstract_inverted_index.expanding | 5 |
| abstract_inverted_index.function. | 94 |
| abstract_inverted_index.mutations | 226 |
| abstract_inverted_index.objective | 222 |
| abstract_inverted_index.orthologs | 125 |
| abstract_inverted_index.potassium | 171 |
| abstract_inverted_index.potential | 179 |
| abstract_inverted_index.proteins. | 167 |
| abstract_inverted_index.variants. | 77 |
| abstract_inverted_index.assessment | 223 |
| abstract_inverted_index.considered | 38 |
| abstract_inverted_index.discovered | 239 |
| abstract_inverted_index.functional | 84 |
| abstract_inverted_index.generation | 82 |
| abstract_inverted_index.hypothesis | 81 |
| abstract_inverted_index.leveraging | 100 |
| abstract_inverted_index.mesophilic | 124 |
| abstract_inverted_index.mutations) | 20 |
| abstract_inverted_index.pathogenic | 161 |
| abstract_inverted_index.sequences. | 29 |
| abstract_inverted_index.sequencing | 2 |
| abstract_inverted_index.structures | 102, 152 |
| abstract_inverted_index.differences | 141 |
| abstract_inverted_index.elucidated. | 15 |
| abstract_inverted_index.identifying | 24 |
| abstract_inverted_index.independent | 158 |
| abstract_inverted_index.large-scale | 40 |
| abstract_inverted_index.protein’s | 93, 132 |
| abstract_inverted_index.sequencing. | 243 |
| abstract_inverted_index.significant | 140 |
| abstract_inverted_index.simulations | 105 |
| abstract_inverted_index.solubility, | 133 |
| abstract_inverted_index.Interpreting | 16 |
| abstract_inverted_index.demonstrates | 219 |
| abstract_inverted_index.distribution | 144 |
| abstract_inverted_index.environment. | 55 |
| abstract_inverted_index.functionally | 14, 72 |
| abstract_inverted_index.interpreting | 75, 236 |
| abstract_inverted_index.standardized | 59 |
| abstract_inverted_index.thermophilic | 122 |
| abstract_inverted_index.distributions | 229 |
| abstract_inverted_index.electrostatic | 228 |
| abstract_inverted_index.statistically | 109, 139 |
| abstract_inverted_index.experimentally | 129 |
| abstract_inverted_index.identification | 210 |
| abstract_inverted_index.protein-coding | 28 |
| abstract_inverted_index.time-dependent | 104 |
| abstract_inverted_index.uninterpreted) | 164 |
| abstract_inverted_index.mechanistically | 74 |
| abstract_inverted_index.three-dimensional | 32 |
| cited_by_percentile_year.max | 95 |
| cited_by_percentile_year.min | 91 |
| corresponding_author_ids | https://openalex.org/A5054127002 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 4 |
| corresponding_institution_ids | https://openalex.org/I204308271 |
| citation_normalized_percentile.value | 0.63240979 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |