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VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation.

Silveira SA, Fassio AV, Gonçalves-Almeida VM, de Lima EB, Barcelos YT, Aburjaile FF, Rodrigues LM, Meira W, de Melo-Minardi RC - BMC Proc (2014)

Bottom Line: In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families.More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations.VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil.

ABSTRACT
In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families. More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations. VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.

No MeSH data available.


Related in: MedlinePlus

Manually generated results. Accessibility, betweenness, closeness and degree for manually generated results. Values from Table 1 were normalized by the highest value of the respective column.
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Figure 4: Manually generated results. Accessibility, betweenness, closeness and degree for manually generated results. Values from Table 1 were normalized by the highest value of the respective column.

Mentions: Preliminary results comparing the manual and automatic strategies indicate that it is necessary to improve the fitness function or adjust the genetic algorithm parameters. Figures 4 and 5 show the mutant residues considered harmful for protein function, along with values of centrality measures for both strategies. A total of six mutations were found, namely I20A, K56G, T60K, E153G, N213K and G214P.


VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation.

Silveira SA, Fassio AV, Gonçalves-Almeida VM, de Lima EB, Barcelos YT, Aburjaile FF, Rodrigues LM, Meira W, de Melo-Minardi RC - BMC Proc (2014)

Manually generated results. Accessibility, betweenness, closeness and degree for manually generated results. Values from Table 1 were normalized by the highest value of the respective column.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4155615&req=5

Figure 4: Manually generated results. Accessibility, betweenness, closeness and degree for manually generated results. Values from Table 1 were normalized by the highest value of the respective column.
Mentions: Preliminary results comparing the manual and automatic strategies indicate that it is necessary to improve the fitness function or adjust the genetic algorithm parameters. Figures 4 and 5 show the mutant residues considered harmful for protein function, along with values of centrality measures for both strategies. A total of six mutations were found, namely I20A, K56G, T60K, E153G, N213K and G214P.

Bottom Line: In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families.More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations.VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6.627, 31270-901, Belo Horizonte, Brazil.

ABSTRACT
In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families. More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations. VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.

No MeSH data available.


Related in: MedlinePlus