{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:18:01Z","timestamp":1778055481570,"version":"3.51.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,8,14]],"date-time":"2021-08-14T00:00:00Z","timestamp":1628899200000},"content-version":"vor","delay-in-days":225,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61672541"],"award-info":[{"award-number":["61672541"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972422"],"award-info":[{"award-number":["61972422"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein\u2013nucleic acid complexes play essential roles in regulating transcription, translation, DNA replication, repair and recombination, RNA processing and translocation. Site-directed mutagenesis has been extremely useful in understanding the principles of protein\u2013DNA and protein\u2013RNA interactions, and experimentally determined mutagenesis data are prerequisites for designing effective algorithms for predicting the binding affinity change upon mutation. However, a vital challenge in this area is the lack of sufficient public experimentally recognized mutation data, which leads to difficulties in developing computational prediction methods. In this article, we present Nabe, an integrated database of amino acid mutations and their effects on the binding free energy in protein\u2013DNA and protein\u2013RNA interactions for which binding affinities have been experimentally determined. Compared with existing databases and data sets, Nabe is the largest protein\u2013nucleic acid mutation database, containing 2506 mutations in 473 protein\u2013DNA and protein\u2013RNA complexes, and of that 1751 are alanine mutations in 405 protein\u2013nucleic acid complexes. For researchers to conveniently utilize the data, Nabe assembles protein\u2013DNA and protein\u2013RNA benchmark databases by adopting the data-processing procedures in the majority of models. To further facilitate users to query data, Nabe provides a searchable and graphical web page.<\/jats:p>\n               <jats:p>Database URL: http:\/\/nabe.denglab.org<\/jats:p>","DOI":"10.1093\/database\/baab050","type":"journal-article","created":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T19:13:01Z","timestamp":1627585981000},"source":"Crossref","is-referenced-by-count":10,"title":["Nabe: an energetic database of amino acid mutations in protein\u2013nucleic acid binding interfaces"],"prefix":"10.1093","volume":"2021","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6276-8240","authenticated-orcid":false,"given":"Junyi","family":"Liu","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"},{"name":"Viterbi School of Engineering, University of Southern California, 3650 McClintock Ave. OHE 106, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siyu","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chenzhe","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaping","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuliang","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zixiang","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiacheng","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Wen","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Deng","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University, 22 Shaoshan South Road, Changsha 410075, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,14]]},"reference":[{"key":"2021081407413945100_R1","article-title":"Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks","volume":"19","author":"Pan","year":"2018","journal-title":"BMCGenomics."},{"key":"2021081407413945100_R2","doi-asserted-by":"crossref","first-page":"4","DOI":"10.2174\/1574893611666151119221435","article-title":"An empirical study of features fusion techniques for protein\u2013protein interaction prediction","volume":"11","author":"Zeng","year":"2016","journal-title":"Curr. 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