{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:06:39Z","timestamp":1778058399486,"version":"3.51.4"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,2,20]],"date-time":"2018-02-20T00:00:00Z","timestamp":1519084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Cl\u00e9ment Viricel"},{"name":"French \u2018R\u00e9gion Occitanie"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Using guaranteed Cost Function Network algorithms, Rosetta energy functions and Dunbrack\u2019s rotamer library, we developed and assessed EasyE and JayZ, two methods for binding affinity estimation that ignore or include conformational entropic contributions on a large benchmark of binding affinity experimental measures. If both approaches outperform most established tools, we observe that side-chain conformational entropy brings little or no improvement on most systems but becomes crucial in some rare cases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>as open-source Python\/C++\u2009code at sourcesup.renater.fr\/projects\/easy-jayz.<\/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\/bty092","type":"journal-article","created":{"date-parts":[[2018,2,16]],"date-time":"2018-02-16T20:11:36Z","timestamp":1518811896000},"page":"2581-2589","source":"Crossref","is-referenced-by-count":13,"title":["Cost function network-based design of protein\u2013protein interactions: predicting changes in binding affinity"],"prefix":"10.1093","volume":"34","author":[{"given":"Cl\u00e9ment","family":"Viricel","sequence":"first","affiliation":[{"name":"Laboratoire d\u2019Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France"},{"name":"Unit\u00e9 de Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse, INRA, Castanet Tolosan cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon","family":"de Givry","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse, INRA, Castanet Tolosan cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Schiex","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse, INRA, Castanet Tolosan cedex, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophie","family":"Barbe","sequence":"additional","affiliation":[{"name":"Laboratoire d\u2019Ing\u00e9nierie des Syst\u00e8mes Biologiques et des Proc\u00e9d\u00e9s, Universit\u00e9 de Toulouse, CNRS, INRA, INSA, Toulouse, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,2,20]]},"reference":[{"key":"2023012713063528100_bty092-B1","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1021\/acs.jctc.7b00125","article-title":"The rosetta all-atom energy function for macromolecular modeling and design","volume":"13","author":"Alford","year":"2017","journal-title":"J. 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