Biophysical and mechanistic models for disease-causing protein variants

A Stein, DM Fowler, R Hartmann-Petersen… - Trends in biochemical …, 2019 - cell.com
The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In
medicine, genome sequencing has revealed millions of missense variants that change …

Rhapsody: predicting the pathogenicity of human missense variants

L Ponzoni, DA Peñaherrera, ZN Oltvai, I Bahar - Bioinformatics, 2020 - academic.oup.com
Motivation The biological effects of human missense variants have been studied
experimentally for decades but predicting their effects in clinical molecular diagnostics …

Toward mechanistic models for genotype–phenotype correlations in phenylketonuria using protein stability calculations

R Scheller, A Stein, SV Nielsen, FI Marin… - Human …, 2019 - Wiley Online Library
Phenylketonuria (PKU) is a genetic disorder caused by variants in the gene encoding
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 …

Toward inferring Potts models for phylogenetically correlated sequence data

E Rodriguez Horta, P Barrat-Charlaix, M Weigt - Entropy, 2019 - mdpi.com
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 …

Interpreting the molecular mechanisms of disease variants in human transmembrane proteins

JKS Tiemann, H Zschach, K Lindorff-Larsen, A Stein - Biophysical Journal, 2023 - cell.com
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 …

Classifying disease-associated variants using measures of protein activity and stability

MM Jepsen, DM Fowler, R Hartmann-Petersen… - Protein homeostasis …, 2020 - Elsevier
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 …

Multiplexed assays reveal effects of missense variants in MSH2 and cancer predisposition

SV Nielsen, R Hartmann-Petersen, A Stein… - PLoS …, 2021 - journals.plos.org
DNA sequencing plays an increasingly central role in clinical research and diagnostics.
Genome-wide association studies have established many links between genes and disease …

AFFIPred: AlphaFold2 structure‐based Functional Impact Prediction of missense variations

MS Pir, E Timucin - Protein Science, 2025 - Wiley Online Library
Protein structure holds immense potential for pathogenicity prediction, albeit structure‐
based predictors are limited compared to the sequence‐based counterparts due to the …

Mean dimension of generative models for protein sequences

C Feinauer, E Borgonovo - bioRxiv, 2022 - biorxiv.org
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 …