ArticleBMC bioinformatics2007
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed, 23 citations in OpenAlex.
- SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites.PLoS computational biology · 2022Article
- Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of glycoside hydrolase.BMC bioinformatics · 2014Article
- Article
- Binding ligand prediction for proteins using partial matching of local surface patches.International journal of molecular sciences · 2010Article
- Structural motifs recurring in different folds recognize the same ligand fragments.BMC bioinformatics · 2009Article
- CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships.Genome biology · 2008Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundWe performed an exhaustive search for local structural similarities in an ensemble of non-redundant protein functional sites. With the purpose of finding new examples of convergent evolution, we selected only those matching sites composed of structural regions whose residue order is inverted in the relative protein sequences.
resultsA novel case of local analogy was detected between members of the ABC transporter and of the HprK/P families in their ATP binding site. This case cannot be derived by events of circular permutation since the residues of one of the region pairs are located in reverse order in the sequence of the two protein families. One of the analogous binding sites, the one identified in HprK/P, is known to also bind pyrophosphate, which is used as preferred energy source in its kinase and phosphorylase activity.
conclusionThe discovery of this striking molecular similarity, also associated to a functional similarity, may help in suggesting new experiments aimed at a deeper understanding of members of the ABC transporter family known to be involved in many serious human diseases.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.