A guide to machine learning for biologists

JG Greener, SM Kandathil, L Moffat… - Nature reviews Molecular …, 2022 - nature.com
The expanding scale and inherent complexity of biological data have encouraged a growing
use of machine learning in biology to build informative and predictive models of the …

Artificial intelligence challenges for predicting the impact of mutations on protein stability

F Pucci, M Schwersensky, M Rooman - Current opinion in structural biology, 2022 - Elsevier
Stability is a key ingredient of protein fitness, and its modification through targeted mutations
has applications in various fields, such as protein engineering, drug design, and deleterious …

DDMut: predicting effects of mutations on protein stability using deep learning

Y Zhou, Q Pan, DEV Pires… - Nucleic Acids …, 2023 - academic.oup.com
Understanding the effects of mutations on protein stability is crucial for variant interpretation
and prioritisation, protein engineering, and biotechnology. Despite significant efforts …

A structural biology community assessment of AlphaFold2 applications

M Akdel, DEV Pires, EP Pardo, J Jänes… - Nature Structural & …, 2022 - nature.com
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …

DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations

CHM Rodrigues, DEV Pires, DB Ascher - Protein Science, 2021 - Wiley Online Library
Predicting the effect of missense variations on protein stability and dynamics is important for
understanding their role in diseases, and the link between protein structure and function …

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

CHM Rodrigues, DEV Pires… - Nucleic acids research, 2018 - academic.oup.com
Proteins are highly dynamic molecules, whose function is intrinsically linked to their
molecular motions. Despite the pivotal role of protein dynamics, their computational …

[HTML][HTML] Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated?

S Ittisoponpisan, SA Islam, T Khanna, E Alhuzimi… - Journal of molecular …, 2019 - Elsevier
Abstract Knowledge of protein structure can be used to predict the phenotypic consequence
of a missense variant. Since structural coverage of the human proteome can be roughly …

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

CHM Rodrigues, Y Myung, DEV Pires… - Nucleic acids …, 2019 - academic.oup.com
Protein–protein Interactions are involved in most fundamental biological processes, with
disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a …

ACE2 gene variants may underlie interindividual variability and susceptibility to COVID-19 in the Italian population

E Benetti, R Tita, O Spiga, A Ciolfi, G Birolo… - European Journal of …, 2020 - nature.com
In December 2019, an initial cluster of interstitial bilateral pneumonia emerged in Wuhan,
China. A human-to-human transmission was assumed and a previously unrecognized entity …

SDM: a server for predicting effects of mutations on protein stability

AP Pandurangan, B Ochoa-Montano… - Nucleic acids …, 2017 - academic.oup.com
Here, we report a webserver for the improved SDM, used for predicting the effects of
mutations on protein stability. As a pioneering knowledge-based approach, SDM has been …