ArticleBMC biochemistry2011
Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates.
Article in BMC biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 29 citations in OpenAlex.
- A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.Briefings in bioinformatics · 2024Review
- SortPred: The first machine learning based predictor to identify bacterial sortases and their classes using sequence-derived information.Computational and structural biotechnology journal · 2022Article
- Label-Free Time-Gated Luminescent Detection Method for the Nucleotides with Varying Phosphate Content.Sensors (Basel, Switzerland) · 2018Article
- Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.Nucleic acids research · 2018Article
- Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives.Frontiers in plant science · 2015Article
- Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble.BMC bioinformatics · 2014Article
- A new supervised over-sampling algorithm with application to protein-nucleotide binding residue prediction.PloS one · 2014Article
- ATP synthase: the right size base model for nanomotors in nanomedicine.TheScientificWorldJournal · 2014Review
- ATP synthase: a molecular therapeutic drug target for antimicrobial and antitumor peptides.Current medicinal chemistry · 2013Review
- Molecular basis for nucleotide conservation at the ends of the dengue virus genome.PLoS pathogens · 2012Article
- Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features.BMC bioinformatics · 2012Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundAdenine and guanine phosphates are involved in a number of biological processes such as cell signaling, metabolism and enzymatic cofactor functions. Binding sites in proteins for these ligands are often detected by looking for a previously known motif by alignment based search. This is likely to miss those where a similar binding site has not been previously characterized and when the binding sites do not follow the rule described by predefined motif. Also, it is intriguing how proteins select between adenine and guanine derivative with high specificity.
resultsResidue preferences for AMP, GMP, ADP, GDP, ATP and GTP have been investigated in details with additional comparison with cyclic variants cAMP and cGMP. We also attempt to predict residues interacting with these nucleotides using information derived from local sequence and evolutionary profiles. Results indicate that subtle differences exist between single residue preferences for specific nucleotides and taking neighbor environment and evolutionary context into account, successful models of their binding site prediction can be developed.
conclusionIn this work, we explore how single amino acid propensities for these nucleotides play a role in the affinity and specificity of this set of nucleotides. This is expected to be helpful in identifying novel binding sites for adenine and guanine phosphates, especially when a known binding motif is not detectable.
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