{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T22:00:39Z","timestamp":1777932039737,"version":"3.51.4"},"reference-count":108,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,2,5]],"date-time":"2020-02-05T00:00:00Z","timestamp":1580860800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Government of the Russian Federation"},{"name":"ITMO Fellowship"},{"name":"Professorship Program","award":["08-08"],"award-info":[{"award-number":["08-08"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Halides are negatively charged ions of halogens, forming fluorides (F\u2212), chlorides (Cl\u2212), bromides (Br\u2212) and iodides (I\u2212). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide\u2013protein interactions, based on the entries in the Protein Data Bank.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide\u2013protein interactions and assist phasing experiments relying on halides as anomalous scatters.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All data described in this article can be reproduced via complied pipeline published at https:\/\/github.com\/rostkick\/Halide_sites\/blob\/master\/README.md.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa079","type":"journal-article","created":{"date-parts":[[2020,1,29]],"date-time":"2020-01-29T12:15:54Z","timestamp":1580300154000},"page":"3064-3071","source":"Crossref","is-referenced-by-count":22,"title":["Census of halide-binding sites in protein structures"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7203-8206","authenticated-orcid":false,"given":"Rostislav K","family":"Skitchenko","sequence":"first","affiliation":[{"name":"Institute BioEngineering, ITMO University , Saint-Petersburg 197101, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dmitrii","family":"Usoltsev","sequence":"additional","affiliation":[{"name":"Institute BioEngineering, ITMO University , Saint-Petersburg 197101, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mayya","family":"Uspenskaya","sequence":"additional","affiliation":[{"name":"Institute BioEngineering, ITMO University , Saint-Petersburg 197101, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrey V","family":"Kajava","sequence":"additional","affiliation":[{"name":"Institute BioEngineering, ITMO University , Saint-Petersburg 197101, Russia"},{"name":"Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Universite Montpellier , Montpellier 34293, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2340-2216","authenticated-orcid":false,"given":"Albert","family":"Guskov","sequence":"additional","affiliation":[{"name":"Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen , Groningen 9747 AG, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,2,5]]},"reference":[{"key":"2023013111532775200_btaa079-B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s10969-011-9101-7","article-title":"SAD phasing using iodide ions in a high-throughput structural genomics environment","volume":"12","author":"Abendroth","year":"2011","journal-title":"J. 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