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Biophysical and mechanistic models for disease-causing protein variants
The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In
medicine, genome sequencing has revealed millions of missense variants that change …
medicine, genome sequencing has revealed millions of missense variants that change …
Rhapsody: predicting the pathogenicity of human missense variants
Motivation The biological effects of human missense variants have been studied
experimentally for decades but predicting their effects in clinical molecular diagnostics …
experimentally for decades but predicting their effects in clinical molecular diagnostics …
Toward mechanistic models for genotype–phenotype correlations in phenylketonuria using protein stability calculations
Phenylketonuria (PKU) is a genetic disorder caused by variants in the gene encoding
phenylalanine hydroxylase (PAH), resulting in accumulation of phenylalanine to neurotoxic …
phenylalanine hydroxylase (PAH), resulting in accumulation of phenylalanine to neurotoxic …
Understanding structure-guided variant effect predictions using 3D convolutional neural networks
G Ramakrishnan, C Baakman, S Heijl… - Frontiers in molecular …, 2023 - frontiersin.org
Predicting pathogenicity of missense variants in molecular diagnostics remains a challenge
despite the available wealth of data, such as evolutionary information, and the wealth of …
despite the available wealth of data, such as evolutionary information, and the wealth of …
Toward inferring Potts models for phylogenetically correlated sequence data
Global coevolutionary models of protein families have become increasingly popular due to
their capacity to predict residue–residue contacts from sequence information, but also to …
their capacity to predict residue–residue contacts from sequence information, but also to …
Interpreting the molecular mechanisms of disease variants in human transmembrane proteins
Next-generation sequencing of human genomes reveals millions of missense variants,
some of which may lead to loss of protein function and ultimately disease. Here, we …
some of which may lead to loss of protein function and ultimately disease. Here, we …
Classifying disease-associated variants using measures of protein activity and stability
The decreased cost of human exome and genome sequencing provides new opportunities
for diagnosing genetic disorders. In order to utilize this information, we need better and more …
for diagnosing genetic disorders. In order to utilize this information, we need better and more …
Multiplexed assays reveal effects of missense variants in MSH2 and cancer predisposition
DNA sequencing plays an increasingly central role in clinical research and diagnostics.
Genome-wide association studies have established many links between genes and disease …
Genome-wide association studies have established many links between genes and disease …
AFFIPred: AlphaFold2 structure‐based Functional Impact Prediction of missense variations
Protein structure holds immense potential for pathogenicity prediction, albeit structure‐
based predictors are limited compared to the sequence‐based counterparts due to the …
based predictors are limited compared to the sequence‐based counterparts due to the …
Mean dimension of generative models for protein sequences
Generative models for protein sequences are important for protein design, mutational effect
prediction and structure prediction. In all of these tasks, the introduction of models which …
prediction and structure prediction. In all of these tasks, the introduction of models which …