2021
DOI: 10.1093/nar/gkab848
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ProNAB: database for binding affinities of protein–nucleic acid complexes and their mutants

Abstract: Protein–nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation and packaging. The binding affinities of protein–DNA and protein–RNA complexes are important for elucidating the mechanism of protein–nucleic acid recognition. Although experimental data on binding affinity are reported abundantly in the literature, no well-curated database is currently available for protein–nucleic acid binding affinity. We have developed a database, … Show more

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Cited by 33 publications
(35 citation statements)
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“…Finally, two new databases curate information previously only inconveniently scattered through the literature. dNTPpoolDB contains concentrations of deoxyribonucleotide triphosphates in different species, cells and experimental conditions ( 111 ) while ProNAB contains >20 000 data points on binding affinity of proteins (wild-type and mutant) for DNA or RNA ( 112 ).…”
Section: New and Updated Databasesmentioning
confidence: 99%
“…Finally, two new databases curate information previously only inconveniently scattered through the literature. dNTPpoolDB contains concentrations of deoxyribonucleotide triphosphates in different species, cells and experimental conditions ( 111 ) while ProNAB contains >20 000 data points on binding affinity of proteins (wild-type and mutant) for DNA or RNA ( 112 ).…”
Section: New and Updated Databasesmentioning
confidence: 99%
“…This could be caused by inefficient recruitment of the degradation machinery, or it could reflect transient binding of DF proteins to their target mRNAs, such that rapid dissociation from target transcripts does not always allow sufficient time to elicit degradation. Indeed, binding affinities of the YTH domain to m 6 A are in the high nanomolar range (Wang et al 2014; Xu et al 2015; Liu et al 2018), which is on the low end of RNA:protein interaction affinities (Yang et al 2013; Harini et al 2022). In this sense, the idea that all three DF proteins promote degradation is fitting, since it may be a failsafe in case one DF protein binds and dissociates before it can promote degradation.…”
Section: Discussionmentioning
confidence: 99%
“…Later, these features were fed to an XGboost classifier [ 45 ]. Furthermore, Harini et al in 2022 created a database named ProNAB for DNA and protein complexes [ 46 ]. Jia et al, in 2021, proposed KKDBP, a classifier for the prediction of DNA-binding proteins using multiple PSSM feature fusions and random forest as a classifier [ 47 ].…”
Section: Introductionmentioning
confidence: 99%