{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:06:52Z","timestamp":1792800412978,"version":"4.5.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2020,12,14]],"date-time":"2020-12-14T00:00:00Z","timestamp":1607904000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Department of Biotechnology, Government of India"},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["IF170342"],"award-info":[{"award-number":["IF170342"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein\u2013carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein\u2013carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein\u2013carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein\u2013carbohydrate complexes belonging to six categories of protein\u2013carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149\u00a0kcal\/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein\u2013Carbohydrate Affinity Predictor, for predicting the binding affinity of protein\u2013carbohydrate complexes. The web server is freely accessible at https:\/\/web.iitm.ac.in\/bioinfo2\/pcapred\/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera.<\/jats:p>","DOI":"10.1093\/bib\/bbaa319","type":"journal-article","created":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T19:11:44Z","timestamp":1603307504000},"source":"Crossref","is-referenced-by-count":15,"title":["Prediction of protein\u2013carbohydrate complex binding affinity using structural features"],"prefix":"10.1093","volume":"22","author":[{"given":"N R","family":"Siva Shanmugam","sequence":"first","affiliation":[{"name":"Indian Institute of Technology Madras"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J","family":"Jino Blessy","sequence":"additional","affiliation":[{"name":"Indian Institute of Technology Madras"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K","family":"Veluraja","sequence":"additional","affiliation":[{"name":"Indian Institute of Science, Bangalore, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1776-4096","authenticated-orcid":false,"given":"M Michael","family":"Gromiha","sequence":"additional","affiliation":[{"name":"Bharathidasan University, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,14]]},"reference":[{"key":"2021072117042846500_ref1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1002\/jlb.40.1.97","article-title":"Cell-surface carbohydrates in cell recognition and response","volume":"40","author":"Brandley","year":"1986","journal-title":"J Leukoc Biol"},{"key":"2021072117042846500_ref2","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1182\/blood.V88.9.3259.bloodjournal8893259","article-title":"Selectins and their ligands: current concepts and controversies","volume":"88","author":"Kansas","year":"1996","journal-title":"Blood"},{"key":"2021072117042846500_ref3","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/978-1-4615-1267-7_28","volume-title":"The Molecular Immunology of Complex Carbohydrates-2. 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