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Computational prediction and interpretation of the molecular effect and disease phenotype of missense variants in the human exome Vrije Universiteit Brussel

François Ancien
Despite the advent of new high-throughput experimental methods and the incredible amount of data they produce, it remains challenging to understand the link between inherited diseases, their genetic causes, and the impact of variants on protein structure, stability, and function. While many bioinformatics tools predict which variants in the human exome are likely to cause diseases, few tools predict the molecular causes of these phenotypes. ...

MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome Vrije Universiteit Brussel

François Ancien, Fabrizio Pucci, Wim Vranken, Marianne Rooman

MOTIVATION: High-throughput experiments are generating ever increasing amounts of various -omics data, so shedding new light on the link between human disorders, their genetic causes, and the related impact on protein behavior and structure. While numerous bioinformatics tools now exist that predict which variants in the human exome cause diseases, few tools predict the reasons why they might do so. Yet, understanding the impact of variants ...

SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs Vrije Universiteit Brussel

Fabrizio Pucci, François Ancien, Jean Marc Kwasigroch, Raphaël Bourgeas
Motivation

Although structured proteins adopt their lowest free energy conformation in physiological conditions, the individual residues are generally not in their lowest free energy conformation. Residues that are stability weaknesses are often involved in functional regions, whereas stability strengths ensure local structural stability. The detection of strengths and weaknesses provides key information to guide protein engineering ...

In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity Vrije Universiteit Brussel

François Ancien, Fabrizio Pucci, Marianne Rooman

Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we ...

Prediction and interpretation of deleterious coding variants in terms of protein structural stability Vrije Universiteit Brussel

François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman

The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses ...