BALCONY: an R package for MSA and functional compartments of protein variability analysis

Płuciennik, Alicja; Stolarczyk, Michał; Bzówka, Maria; Raczyńska, Agata; Magdziarz, Tomasz; Góra, Artur

doi:10.1186/s12859-018-2294-z

Cited by 12 publications

(15 citation statements)

References 24 publications

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“…Color scale is further explained in Section 2. Alignment consensus is shown in grayscale underneath the plot as measured by evolutionary trace (Płuciennik et al., ; Wilkins, Erdin, Lua, & Lichtarge, ), with high consensus positions in black and low consensus in white. Key functional domains are outlined in black and labeled above the plot.…”

Section: Resultsmentioning

confidence: 99%

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Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

et al. 2019

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Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project ( http://1001genomes.org ). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well‐studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well‐studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less‐studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/ ) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/ ).

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Section: Resultsmentioning

confidence: 99%

“…Color scale is explained in Section 2. In grayscale underneath the plot, alignment consensus is shown as measured by Evolutionary trace (Płuciennik et al., ; Wilkins et al., ), with high‐consensus positions in black and low consensus in white…”

Section: Resultsmentioning

confidence: 99%

Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

et al. 2019

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“…The Multiple Sequence Alignment (MSA) of 312 sequences of close homologues of soluble epoxide hydrolases deposited with the BALCONY (Better ALignment CONsensus analYsis) package [38] was downloaded to perform an evolutionary study. Prior to analysis, the MSA was truncated.…”

Section: Resultsmentioning

confidence: 99%

“…Close inspection suggested a large difference between the entropy scores of residues making up particular cavities (Figure 7a–c). The analytic comparisons were carried out with Kolmogorov-Smirnov tests in a similar way to that reported elsewhere [38]. According to the test results, the cavities indeed presented different evolutionary rates.…”

Section: Resultsmentioning

confidence: 99%

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Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking

et al. 2018

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Several different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations and a water tracking approach to describe the water accessible volume of Solanum tuberosum epoxide hydrolase. Using water as a molecular probe, we were able to identify small cavities linked with the active site: (i) one made up of conserved amino acids and indispensable for the proper positioning of catalytic water and (ii) two others in which modification can potentially contribute to enzyme selectivity and activity. Additionally, we identified regions suitable for de novo tunnel design that could also modify the catalytic properties of the enzyme. The identified hot-spots extend the list of the previously targeted residues used for modification of the regioselectivity of the enzyme. Finally, we have provided an example of a simple and elegant process for the detailed description of the network of cavities and tunnels, which can be used in the planning of enzyme modifications and can be easily adapted to the study of any other protein.

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Llama peripheral B-cell populations producing conventional and heavy chain-only IgG subtypes are phenotypically indistinguishable but immunogenetically distinct

et al. 2019

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BALCONY: an R package for MSA and functional compartments of protein variability analysis

Cited by 12 publications

References 24 publications

Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking

Llama peripheral B-cell populations producing conventional and heavy chain-only IgG subtypes are phenotypically indistinguishable but immunogenetically distinct

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