ArticleProteome science2012
Modeling regionalized volumetric differences in protein-ligand binding cavities.
Article in Proteome science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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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.
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Who cites it
4 citing papers in PubMed.
- Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials.Algorithms for molecular biology : AMB · 2020Article
- VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.PLoS computational biology · 2014Article
- An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.BMC structural biology · 2013Article
- Reflection on design and testing of pancreatic alpha-amylase inhibitors: an in silico comparison between rat and rabbit enzyme models.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying elements of protein structures that create differences in protein-ligand binding specificity is an essential method for explaining the molecular mechanisms underlying preferential binding. In some cases, influential mechanisms can be visually identified by experts in structural biology, but subtler mechanisms, whose significance may only be apparent from the analysis of many structures, are harder to find. To assist this process, we present a geometric algorithm and two statistical models for identifying significant structural differences in protein-ligand binding cavities. We demonstrate these methods in an analysis of sequentially nonredundant structural representatives of the canonical serine proteases and the enolase superfamily. Here, we observed that statistically significant structural variations identified experimentally established determinants of specificity. We also observed that an analysis of individual regions inside cavities can reveal areas where small differences in shape can correspond to differences in specificity.
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Registered trials
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