Genome interpretation using in silico predictors of variant impact
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …
personalized therapeutic opportunities. Clinical associations and laboratory experiments …
Interpreting protein variant effects with computational predictors and deep mutational scanning
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 …
These programs provide clinical and research laboratories with a rapid and scalable method …
REVEL: an ensemble method for predicting the pathogenicity of rare missense variants
The vast majority of coding variants are rare, and assessment of the contribution of rare
variants to complex traits is hampered by low statistical power and limited functional data …
variants to complex traits is hampered by low statistical power and limited functional data …
Predicting secretory proteins with SignalP
H Nielsen - Protein function prediction: methods and protocols, 2017 - Springer
SignalP is the currently most widely used program for prediction of signal peptides from
amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway …
amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway …
Updated benchmarking of variant effect predictors using deep mutational scanning
The assessment of variant effect predictor (VEP) performance is fraught with biases
introduced by benchmarking against clinical observations. In this study, building on our …
introduced by benchmarking against clinical observations. In this study, building on our …
Embeddings from protein language models predict conservation and variant effects
The emergence of SARS-CoV-2 variants stressed the demand for tools allowing to interpret
the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational …
the effect of single amino acid variants (SAVs) on protein function. While Deep Mutational …
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update
We present here a full update of the PMut predictor, active since 2005 and with a large
acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine …
acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine …
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
To deal with the huge number of novel protein‐coding variants identified by genome and
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
How good are pathogenicity predictors in detecting benign variants?
Computational tools are widely used for interpreting variants detected in sequencing
projects. The choice of these tools is critical for reliable variant impact interpretation for …
projects. The choice of these tools is critical for reliable variant impact interpretation for …
Variation interpretation predictors: principles, types, performance, and choice
Next‐generation sequencing methods have revolutionized the speed of generating variation
information. Sequence data have a plethora of applications and will increasingly be used for …
information. Sequence data have a plethora of applications and will increasingly be used for …