{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T11:12:39Z","timestamp":1783768359140,"version":"3.55.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T00:00:00Z","timestamp":1777852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Science Foundation, Division of Information & Intelligent Systems","award":["NSF-2444456"],"award-info":[{"award-number":["NSF-2444456"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein\u2013protein interactions and therapeutic drug design. Here, we present SPICE (Structural Protein Interaction Complex Evaluator), a web-based platform that allows structural biologists to perform rapid, modular analyses of protein complexes directly from Protein Data Bank (PDB) structures. SPICE allows users to define and execute analysis workflows via an intuitive web interface, reducing analysis times from minutes to seconds. The platform offers a broad range of analytical capabilities, including (i) detection of hydrogen bonds, salt bridges, and disulfide bonds; (ii) protein\u2013protein interface mapping; and (iii) computation of solvent accessibility, van der Waals energetics, and other key geometric descriptors. SPICE further provides interactive 3D visualization and supports comparative analyses across multiple complexes, enabling the study of mutational effects and binding variants. The tool is freely available at https:\/\/spice.cs.ucr.edu (no registration required).<\/jats:p>","DOI":"10.1093\/nar\/gkag415","type":"journal-article","created":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T11:32:06Z","timestamp":1776771126000},"page":"W321-W326","source":"Crossref","is-referenced-by-count":1,"title":["Comparative structural analysis of protein complexes with SPICE"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4006-5389","authenticated-orcid":false,"given":"Faisal Bin","family":"Ashraf","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of California , Riverside 92521, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2696-7274","authenticated-orcid":false,"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of California , Riverside 92521, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,4]]},"reference":[{"key":"2026071106371891400_B1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1073\/pnas.93.1.13","article-title":"Principles of protein\u2013protein interactions","volume":"93","author":"Jones","year":"1996","journal-title":"Proc Natl Acad Sci"},{"key":"2026071106371891400_B2","doi-asserted-by":"publisher","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":"2026071106371891400_B3","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1016\/j.jmb.2007.05.022","article-title":"Inference of macromolecular assemblies from crystalline state","volume":"372","author":"Krissinel","year":"2007","journal-title":"J Mol Biol"},{"key":"2026071106371891400_B4","doi-asserted-by":"publisher","first-page":"W314","DOI":"10.1093\/nar\/gkv314","article-title":"Stock-based detection of protein oligomeric states in jsPISA","volume":"43","author":"Krissinel","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026071106371891400_B5","doi-asserted-by":"publisher","first-page":"W473","DOI":"10.1093\/nar\/gkm423","article-title":"PIC: protein interactions calculator","volume":"35","author":"Tina","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2026071106371891400_B6","doi-asserted-by":"publisher","first-page":"e07454","DOI":"10.7554\/eLife.07454","article-title":"Contacts-based prediction of binding affinity in protein\u2013protein complexes","volume":"4","author":"Vangone","year":"2015","journal-title":"elife"},{"key":"2026071106371891400_B7","doi-asserted-by":"publisher","first-page":"W474","DOI":"10.1093\/nar\/gkac307","article-title":"MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes","volume":"50","author":"Badaczewska-Dawid","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026071106371891400_B8","doi-asserted-by":"publisher","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":"2026071106371891400_B9","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1002\/1439-7633(20020703)3","article-title":"Close-range electrostatic interactions in proteins","volume":"3","author":"Kumar","year":"2002","journal-title":"ChemBioChem"},{"key":"2026071106371891400_B10","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1002\/pro.5560021002","article-title":"Disulfide bonds and the stability of globular proteins","volume":"2","author":"Betz","year":"1993","journal-title":"Protein Sci"},{"key":"2026071106371891400_B11","doi-asserted-by":"publisher","first-page":"189","DOI":"10.12688\/f1000research.7931.1","article-title":"FreeSASA: an open source C library for solvent accessible surface area calculations","volume":"5","author":"Mitternacht","year":"2016","journal-title":"F1000Research"},{"key":"2026071106371891400_B12","doi-asserted-by":"publisher","first-page":"20120835","DOI":"10.1098\/rsif.2012.0835","article-title":"On the binding affinity of macromolecular interactions: daring to ask why proteins interact","volume":"10","author":"Kastritis","year":"2013","journal-title":"J Roy Soc Interface"},{"key":"2026071106371891400_B13","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1016\/j.jmb.2010.09.028","article-title":"A simple definition of structural regions in proteins and its use in analyzing interface evolution","volume":"403","author":"Levy","year":"2010","journal-title":"J Mol Biol"},{"key":"2026071106371891400_B14","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","article-title":"3Dmol. js: molecular visualization with WebGL","volume":"31","author":"Rego","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/W1\/W321\/68205358\/gkag415.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/W1\/W321\/68205358\/gkag415.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T10:37:25Z","timestamp":1783766245000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/54\/W1\/W321\/8666724"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,4]]},"references-count":14,"journal-issue":{"issue":"W1","published-print":{"date-parts":[[2026,7,11]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkag415","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7,7]]},"published":{"date-parts":[[2026,5,4]]}}}