{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:56:10Z","timestamp":1760241370519,"version":"build-2065373602"},"reference-count":12,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2018,1,13]],"date-time":"2018-01-13T00:00:00Z","timestamp":1515801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["8UL1TR000077"],"award-info":[{"award-number":["8UL1TR000077"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Similarity and distance matrices are general data structures that describe reciprocal relationships between the objects within a given dataset. Commonly used methods for representation of these matrices include heatmaps, hierarchical trees, dimensionality reduction, and various types of networks. However, despite a well-developed foundation for the visualization of such representations, the challenge of creating an interactive view that would allow for quick data navigation and interpretation remains largely unaddressed. This problem becomes especially evident for large matrices with hundreds or thousands objects. In this work, we present a web-based platform for the interactive analysis of large (dis-)similarity matrices. It consists of four major interconnected and synchronized components: a zoomable heatmap, interactive hierarchical tree, scalable circular relationship diagram, and 3D multi-dimensional scaling (MDS) scatterplot. We demonstrate the use of the platform for the analysis of amino acid covariance data in proteins as part of our previously developed CoeViz tool. The web-platform enables quick and focused analysis of protein features, such as structural domains and functional sites.<\/jats:p>","DOI":"10.3390\/data3010004","type":"journal-article","created":{"date-parts":[[2018,1,15]],"date-time":"2018-01-15T12:30:36Z","timestamp":1516019436000},"page":"4","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices"],"prefix":"10.3390","volume":"3","author":[{"given":"Frazier","family":"Baker","sequence":"first","affiliation":[{"name":"Department of Electrical Engineering and Computing Systems, University of Cincinnati, Cincinnati, OH 45221, USA"},{"name":"Center for Autoimmune Genomics and Etiology, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH 45229, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3202-5099","authenticated-orcid":false,"given":"Aleksey","family":"Porollo","sequence":"additional","affiliation":[{"name":"Center for Autoimmune Genomics and Etiology, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH 45229, USA"},{"name":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center, Cincinnati, OH 45229, USA"},{"name":"Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA"}]}],"member":"1968","published-online":{"date-parts":[[2018,1,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Baker, F.N., and Porollo, A. (2016). CoeViz: A web-based tool for coevolution analysis of protein residues. BMC Bioinform., 17.","DOI":"10.1186\/s12859-016-0975-z"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/bth248","article-title":"Polyview: A flexible visualization tool for structural and functional annotations of proteins","volume":"20","author":"Porollo","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Porollo, A., and Meller, J. (2007). Versatile annotation and publication quality visualization of protein complexes using polyview-3D. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-316"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1250","DOI":"10.1107\/S0021889810030256","article-title":"Jmol\u2014A paradigm shift in crystallographic visualization","volume":"43","author":"Hanson","year":"2010","journal-title":"J. Appl. Crystallogr."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Adhikari, B., Nowotny, J., Bhattacharya, D., Hou, J., and Cheng, J. (2016). Coneva: A toolbox for comprehensive assessment of protein contacts. BMC Bioinform., 17.","DOI":"10.1186\/s12859-016-1404-z"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1038\/nbt.2419","article-title":"Protein structure prediction from sequence variation","volume":"30","author":"Marks","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e02030","DOI":"10.7554\/eLife.02030","article-title":"Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information","volume":"3","author":"Ovchinnikov","year":"2014","journal-title":"Elife"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D-3: Data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. Vis. Comput. Graph."},{"key":"ref_9","unstructured":"Ooms, J., Temple Lang, D., and Hilaiel, L. (2018, January 12). Jsonlite: A Robust, High Performance JSON Parser and Generator for R. Available online: https:\/\/cran.r-project.org\/web\/packages\/jsonlite\/index.html."},{"key":"ref_10","unstructured":"Adler, D., Nenadic, O., and Zucchini, W. (2003, January 12\u201315). RGL: A R-library for 3D visualization with OpenGL. Proceedings of the 35th Symposium of the Interface: Computing Science and Statistics, Salt Lake City, UT, USA."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1002\/prot.21248","article-title":"Prediction-based fingerprints of protein-protein interactions","volume":"66","author":"Porollo","year":"2007","journal-title":"Proteins"}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/1\/4\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T14:51:08Z","timestamp":1760194268000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/1\/4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,1,13]]},"references-count":12,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,3]]}},"alternative-id":["data3010004"],"URL":"https:\/\/doi.org\/10.3390\/data3010004","relation":{},"ISSN":["2306-5729"],"issn-type":[{"type":"electronic","value":"2306-5729"}],"subject":[],"published":{"date-parts":[[2018,1,13]]}}}