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dc.contributor.authorSharma, Ronesh
dc.contributor.authorKumar, Shiu
dc.contributor.authorTsunoda, Tatsuhiko
dc.contributor.authorKumarevel, Thirumananseri
dc.contributor.authorSharma, Alok
dc.date.accessioned2020-10-06T01:17:48Z
dc.date.available2020-10-06T01:17:48Z
dc.date.issued2020
dc.identifier.issn0003-2697
dc.identifier.doi10.1016/j.ab.2020.113954
dc.identifier.urihttp://hdl.handle.net/10072/398100
dc.description.abstractBackground: DNA-binding proteins perform important roles in cellular processes and are involved in many biological activities. These proteins include crucial protein-DNA binding domains and can interact with single-stranded or double-stranded DNA, and accordingly classified as single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins (DSBs). Computational prediction of SSBs and DSBs helps in annotating protein functions and understanding of protein-binding domains. Results: Performance is reported using the DNA-binding protein dataset that was recently introduced by Wang et al., [1]. The proposed method achieved a sensitivity of 0.600, specificity of 0.792, AUC of 0.758, MCC of 0.369, accuracy of 0.744, and F-measure of 0.536, on the independent test set. Conclusion: The proposed method with the hidden Markov model (HMM) profiles for feature extraction, outperformed the benchmark method in the literature and achieved an overall improvement of approximately 3%. The source code and supplementary information of the proposed method is available at https://github.com/roneshsharma/Predict-DNA-binding-proteins/wiki.
dc.description.peerreviewedYes
dc.languageEnglish
dc.language.isoeng
dc.publisherElsevier
dc.relation.ispartofjournalAnalytical Biochemistry
dc.relation.ispartofvolume612
dc.subject.fieldofresearchAnalytical chemistry
dc.subject.fieldofresearchOther chemical sciences
dc.subject.fieldofresearchBiochemistry and cell biology
dc.subject.fieldofresearchcode3401
dc.subject.fieldofresearchcode3499
dc.subject.fieldofresearchcode3101
dc.subject.keywordsDNA-binding proteins
dc.subject.keywordsDSBs
dc.subject.keywordsSSBs
dc.subject.keywordshidden Markov model
dc.subject.keywordsk-nearest neighbors
dc.titleSingle-stranded and double-stranded DNA-binding protein prediction using HMM profiles
dc.typeJournal article
dc.type.descriptionC1 - Articles
dcterms.bibliographicCitationSharma, R; Kumar, S; Tsunoda, T; Kumarevel, T; Sharma, A, Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles., Analytical Biochemistry, 2020, 612
dcterms.dateAccepted2020-09-10
dc.date.updated2020-10-01T22:45:23Z
gro.hasfulltextNo Full Text
gro.griffith.authorSharma, Alok


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