VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation
نویسندگان
چکیده
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.
منابع مشابه
PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties
BACKGROUND Non-synonymous single-nucleotide polymorphisms (nsSNPs) within the coding regions of genes causing amino acid substitutions (AASs) may have a large impact on protein function. The possibilities to identify nsSNPs across genomes have increased notably with the advent of next-generation sequencing technologies. Thus, there is a strong need for efficient bioinformatics tools to predict ...
متن کاملParacompactness on supra topological spaces
In this article, we present the concept of supra paracompact spaces and study its basic properties. We elucidate its relationship with supra compact spaces and prove that the property of being a supra paracompact space is weakly hereditary and topological properties. Also, we provide some examples to show some results concerning paracompactness on topology are invalid on supra topology. Finally...
متن کاملInvestigation of GDF9 and BMP15 Polymorphisms in Mehraban Sheep to Find the Missenses as Impact on Protein
Utilization of fecundity genes such as GDF9 and BMP15 can help improve reproductive traits in sheep breeding programme. To evaluate effects of missense mutations on protein function, the polymorphisms of GDF9 and BMP15 genes were screened in twelve mehraban sheep using DNA sequencing, followed by protein structure modeling. Six single nucleotide polymorphism (SNPs) known as FecG mutations (G1-G...
متن کاملQSPR Analysis with Curvilinear Regression Modeling and Topological Indices
Topological indices are the real number of a molecular structure obtained via molecular graph G. Topological indices are used for QSPR, QSAR and structural design in chemistry, nanotechnology, and pharmacology. Moreover, physicochemical properties such as the boiling point, the enthalpy of vaporization, and stability can be estimated by QSAR/QSPR models. In this study, the QSPR (Quantitative St...
متن کاملThe protein-nanoparticle interaction (protein corona) and its importance on the therapeutic application of nanoparticles
Nanobiotechnology has provided promising novel diagnostic and therapeutic strategies which capable to create a broad spectrum of nano-based imaging agents and medicines for human administrations. Several studies have demonstrated that the surface of nanomaterials is immediately coated with suspended proteins after contact with plasma or other biological fluids to form protein corona-nanoparticl...
متن کامل