Interpreting protein variant effects with computational predictors and deep mutational scanning

BJ Livesey, JA Marsh - Disease Models & Mechanisms, 2022 - journals.biologists.com
Computational predictors of genetic variant effect have advanced rapidly in recent years.
These programs provide clinical and research laboratories with a rapid and scalable method …

Automated inference of molecular mechanisms of disease from amino acid substitutions

B Li, VG Krishnan, ME Mort, F Xin, KK Kamati… - …, 2009 - academic.oup.com
Motivation: Advances in high-throughput genotyping and next generation sequencing have
generated a vast amount of human genetic variation data. Single nucleotide substitutions …

Cataloging coding sequence variations in human genome databases

HH Won, HJ Kim, KA Lee, JW Kim - PloS one, 2008 - journals.plos.org
Background With the recent growth of information on sequence variations in the human
genome, predictions regarding the functional effects and relevance to disease phenotypes …

The amino-acid mutational spectrum of human genetic disease

D Vitkup, C Sander, GM Church - Genome biology, 2003 - Springer
Background Nonsynonymous mutations in the coding regions of human genes are
responsible for phenotypic differences between humans and for susceptibility to genetic …

Single nucleotide variations: biological impact and theoretical interpretation

P Katsonis, A Koire, SJ Wilson, TK Hsu, RC Lua… - Protein …, 2014 - Wiley Online Library
Genome‐wide association studies (GWAS) and whole‐exome sequencing (WES) generate
massive amounts of genomic variant information, and a major challenge is to identify which …

Predicting functional consequences of mutations using molecular interaction network features

K Ozturk, H Carter - Human genetics, 2022 - Springer
Variant interpretation remains a central challenge for precision medicine. Missense variants
are particularly difficult to understand as they change only a single amino acid in a protein …

Quantification of the effect of mutations using a global probability model of natural sequence variation

TA Hopf, JB Ingraham, FJ Poelwijk, M Springer… - arXiv preprint arXiv …, 2015 - arxiv.org
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic
functional assays of point mutants of proteins have provided valuable empirical information …

Toward developing intuitive rules for protein variant effect prediction using deep mutational scanning data

CK Sruthi, H Balaram, MK Prakash - ACS omega, 2020 - ACS Publications
Protein structure and function can be severely altered by even a single amino acid mutation.
Predictions of mutational effects using extensive artificial intelligence (AI)-based models …

GEMME: a simple and fast global epistatic model predicting mutational effects

E Laine, Y Karami, A Carbone - Molecular biology and evolution, 2019 - academic.oup.com
The systematic and accurate description of protein mutational landscapes is a question of
utmost importance in biology, bioengineering, and medicine. Recent progress has been …

Structural and functional restraints on the occurrence of single amino acid variations in human proteins

S Gong, TL Blundell - PLOS one, 2010 - journals.plos.org
Human genetic variation is the incarnation of diverse evolutionary history, which reflects
both selectively advantageous and selectively neutral change. In this study, we catalogue …