ArticleNucleic acids research2016
Nucleotide binding database NBDB--a collection of sequence motifs with specific protein-ligand interactions.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Compositionally Biased Regions Within Structured Protein Domains.Biomolecules · 2026Article
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- ATP allosterically regulates an acyl-CoA oxidase.Nature communications · 2025Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- Article
- An evolutionary history of the CoA-binding protein Nat/Ivy.Protein science : a publication of the Protein Society · 2022Review
- Evolution, folding, and design of TIM barrels and related proteins.Current opinion in structural biology · 2021Review
- Deriving and Using Descriptors of Elementary Functions in Rational Protein Design.Frontiers in bioinformatics · 2021Article
- On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment.eLife · 2020Article
- Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- On the evolution of protein-adenine binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Simple yet functional phosphate-loop proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase.The Journal of biological chemistry · 2018Article
- Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain.Nature communications · 2016Article
- The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection.Nucleic acids research · 2016Article
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3 authors.
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Abstract
NBDB database describes protein motifs, elementary functional loops (EFLs) that are involved in binding of nucleotide-containing ligands and other biologically relevant cofactors/coenzymes, including ATP, AMP, ATP, GMP, GDP, GTP, CTP, PAP, PPS, FMN, FAD(H), NAD(H), NADP, cAMP, cGMP, c-di-AMP and c-di-GMP, ThPP, THD, F-420, ACO, CoA, PLP and SAM. The database is freely available online at http://nbdb.bii.a-star.edu.sg. In total, NBDB contains data on 249 motifs that work in interactions with 24 ligands. Sequence profiles of EFL motifs were derived de novo from nonredundant Uniprot proteome sequences. Conserved amino acid residues in the profiles interact specifically with distinct chemical parts of nucleotide-containing ligands, such as nitrogenous bases, phosphate groups, ribose, nicotinamide, and flavin moieties. Each EFL profile in the database is characterized by a pattern of corresponding ligand-protein interactions found in crystallized ligand-protein complexes. NBDB database helps to explore the determinants of nucleotide and cofactor binding in different protein folds and families. NBDB can also detect fragments that match to profiles of particular EFLs in the protein sequence provided by user. Comprehensive information on sequence, structures, and interactions of EFLs with ligands provides a foundation for experimental and computational efforts on design of required protein functions.
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