{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T07:41:54Z","timestamp":1774942914321,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T00:00:00Z","timestamp":1707177600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31991190"],"award-info":[{"award-number":["31991190"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31730052"],"award-info":[{"award-number":["31730052"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31861143042"],"award-info":[{"award-number":["31861143042"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671444"],"award-info":[{"award-number":["31671444"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871352"],"award-info":[{"award-number":["31871352"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0508401"],"award-info":[{"award-number":["2019YFA0508401"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2017YFA0102900"],"award-info":[{"award-number":["2017YFA0102900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this article, we have developed the align distance matrix with scale (ADAMS) pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>ADAMS can be download and used as a python package from Python Package Index (PyPI): adams \u00b7 PyPI. Source code and other materials are available from young55775\/ADAMS-developing (github.com). An online server is available: Bseek Search Server (cryonet.ai)<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae064","type":"journal-article","created":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T23:47:40Z","timestamp":1706831260000},"source":"Crossref","is-referenced-by-count":5,"title":["Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2746-613X","authenticated-orcid":false,"given":"Zhengyang","family":"Guo","sequence":"first","affiliation":[{"name":"Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University , Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Wang","sequence":"additional","affiliation":[{"name":"Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University , Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guangshuo","family":"Ou","sequence":"additional","affiliation":[{"name":"Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University , Beijing 100084, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,6]]},"reference":[{"key":"2024031016391243900_btae064-B1","doi-asserted-by":"crossref","first-page":"e2304302120","DOI":"10.1073\/pnas.2304302120","article-title":"Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2","volume":"120","author":"Alderson","year":"2023","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024031016391243900_btae064-B2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2024031016391243900_btae064-B3","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.sbi.2011.03.011","article-title":"Intrinsically disordered proteins: regulation and disease","volume":"21","author":"Babu","year":"2011","journal-title":"Curr Opin Struct Biol"},{"key":"2024031016391243900_btae064-B4","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2024031016391243900_btae064-B5","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12964-022-00821-7","article-title":"Intrinsically disordered proteins play diverse roles in cell signaling","volume":"20","author":"Bondos","year":"2022","journal-title":"Cell Commun Signal"},{"key":"2024031016391243900_btae064-B6","first-page":"122","article-title":"The OpenCV library","volume":"120","author":"Bradski","year":"2000","journal-title":"Dr Dobb\u2019s Journal of Software Tools"},{"key":"2024031016391243900_btae064-B7","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2024031016391243900_btae064-B8","doi-asserted-by":"crossref","first-page":"167336","DOI":"10.1016\/j.jmb.2021.167336","article-title":"The AlphaFold database of protein structures: a biologist\u2019s guide","volume":"434","author":"David","year":"2022","journal-title":"J Mol Biol"},{"key":"2024031016391243900_btae064-B9","doi-asserted-by":"crossref","first-page":"i718","DOI":"10.1093\/bioinformatics\/btaa839","article-title":"Geometricus represents protein structures as shape-mers derived from moment invariants","volume":"36","author":"Durairaj","year":"2020","journal-title":"Bioinformatics"},{"key":"2024031016391243900_btae064-B10","author":"Greener","year":"2022"},{"key":"2024031016391243900_btae064-B11","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/978-1-0716-0270-6_3","article-title":"Using dali for protein structure comparison","volume":"2112","author":"Holm","year":"2020","journal-title":"Struct Bioinform Methods Protocols"},{"key":"2024031016391243900_btae064-B12","doi-asserted-by":"crossref","first-page":"e4519","DOI":"10.1002\/pro.4519","article-title":"DALI shines a light on remote homologs: one hundred discoveries","volume":"32","author":"Holm","year":"2023","journal-title":"Protein Sci"},{"key":"2024031016391243900_btae064-B13","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1006\/jmbi.1993.1489","article-title":"Protein structure comparison by alignment of distance matrices","volume":"233","author":"Holm","year":"1993","journal-title":"J Mol Biol"},{"key":"2024031016391243900_btae064-B14","doi-asserted-by":"crossref","first-page":"e16059","DOI":"10.7554\/eLife.16059","article-title":"Emergence and evolution of an interaction between intrinsically disordered proteins","volume":"6","author":"Hultqvist","year":"2017","journal-title":"Elife"},{"key":"2024031016391243900_btae064-B15","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2024031016391243900_btae064-B16","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1534\/genetics.118.301307","article-title":"OrthoList 2: a new comparative genomic analysis of human and genes","volume":"210","author":"Kim","year":"2018","journal-title":"Genetics"},{"key":"2024031016391243900_btae064-B17","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2024031016391243900_btae064-B18","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1126\/science.ade2574","article-title":"Evolutionary-scale prediction of atomic-level protein structure with a language model","volume":"379","author":"Lin","year":"2023","journal-title":"Science"},{"key":"2024031016391243900_btae064-B19","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/j.devcel.2008.02.015","article-title":"The SYS-1 protein is a bona fide \u03b2-catenin","volume":"14","author":"Liu","year":"2008","journal-title":"Dev Cell"},{"key":"2024031016391243900_btae064-B20","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1023\/B:VISI.0000029664.99615.94","article-title":"Distinctive image features from scale-invariant keypoints","volume":"60","author":"Lowe","year":"2004","journal-title":"International Journal of Computer Vision"},{"key":"2024031016391243900_btae064-B21","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat Methods"},{"key":"2024031016391243900_btae064-B22","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1093\/protein\/11.9.739","article-title":"Protein structure alignment by incremental combinatorial extension (CE) of the optimal path","volume":"11","author":"Shindyalov","year":"1998","journal-title":"Protein Eng"},{"key":"2024031016391243900_btae064-B23","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol Syst Biol"},{"key":"2024031016391243900_btae064-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pbiomolbio.2016.09.005","article-title":"A review of resolution measures and related aspects in 3D electron microscopy","volume":"124","author":"Sorzano","year":"2017","journal-title":"Prog Biophys Mol Biol"},{"key":"2024031016391243900_btae064-B25","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2024031016391243900_btae064-B26","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gku1028","article-title":"A series of PDB-related databanks for everyday needs","volume":"43","author":"Touw","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2024031016391243900_btae064-B27","doi-asserted-by":"crossref","first-page":"14050","DOI":"10.3390\/ijms232214050","article-title":"Intrinsically disordered proteins: an overview","volume":"23","author":"Trivedi","year":"2022","journal-title":"Ijms"},{"key":"2024031016391243900_btae064-B28","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/s41587-023-01773-0","article-title":"Fast and accurate protein structure search with foldseek","volume":"42","author":"van Kempen","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2024031016391243900_btae064-B29","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1142\/S0219720008003461","article-title":"CLePAPS: fast pair alignment of protein structures based on conformational letters","volume":"6","author":"Wang","year":"2008","journal-title":"J Bioinform Comput Biol"},{"key":"2024031016391243900_btae064-B30","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1093\/nar\/gkl395","article-title":"Protein structure database search and evolutionary classification","volume":"34","author":"Yang","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2024031016391243900_btae064-B31","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1093\/nar\/gki524","article-title":"TM-align: a protein structure alignment algorithm based on the TM-score","volume":"33","author":"Zhang","year":"2005","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae064\/56589010\/btae064.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae064\/56918661\/btae064.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae064\/56918661\/btae064.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,10]],"date-time":"2024-03-10T12:40:06Z","timestamp":1710074406000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae064\/7601449"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2024,2,6]]},"references-count":31,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae064","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.14.566990","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,2,6]]},"article-number":"btae064"}}