Cancer driver mutations: predictions and reality

D Ostroverkhova, TM Przytycka… - Trends in Molecular …, 2023 - cell.com
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of
them drive cancer progression, termed driver mutations. Driver mutations may vary between …

A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation

J Fang - Briefings in bioinformatics, 2020 - academic.oup.com
A number of machine learning (ML)-based algorithms have been proposed for predicting
mutation-induced stability changes in proteins. In this critical review, we used hypothetical …

MutaBind2: predicting the impacts of single and multiple mutations on protein-protein interactions

N Zhang, Y Chen, H Lu, F Zhao, RV Alvarez… - Iscience, 2020 - cell.com
Missense mutations may affect proteostasis by destabilizing or over-stabilizing protein
complexes and changing the pathway flux. Predicting the effects of stabilizing mutations on …

Precision medicine and driver mutations: computational methods, functional assays and conformational principles for interpreting cancer drivers

R Nussinov, H Jang, CJ Tsai… - PLoS computational …, 2019 - journals.plos.org
At the root of the so-called precision medicine or precision oncology, which is our focus
here, is the hypothesis that cancer treatment would be considerably better if therapies were …

Allosteric drugs and mutations: chances, challenges, and necessity

E Guarnera, IN Berezovsky - Current opinion in structural biology, 2020 - Elsevier
Highlights•Allosteric drugs have become an indispensable tool in precision medicine.•Major
targets for allosteric drugs: diversity structures and functions.•Allosteric effects of mutations …

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

M Li, FL Simonetti, A Goncearenco… - Nucleic acids …, 2016 - academic.oup.com
Proteins engage in highly selective interactions with their macromolecular partners.
Sequence variants that alter protein binding affinity may cause significant perturbations or …

Finding driver mutations in cancer: Elucidating the role of background mutational processes

AL Brown, M Li, A Goncearenco… - PLoS computational …, 2019 - journals.plos.org
Identifying driver mutations in cancer is notoriously difficult. To date, recurrence of a mutation
in patients remains one of the most reliable markers of mutation driver status. However …

Molecular biology and evolution of cancer: from discovery to action

JA Somarelli, H Gardner, VL Cannataro… - Molecular biology …, 2020 - academic.oup.com
Cancer progression is an evolutionary process. During this process, evolving cancer cell
populations encounter restrictive ecological niches within the body, such as the primary …

On the perturbation nature of allostery: sites, mutations, and signal modulation

E Guarnera, IN Berezovsky - Current opinion in structural biology, 2019 - Elsevier
Regardless of the diversity of systems, allosteic signalling is found to be always caused by
perturbations. This recurring trait of allostery serves as a foundation for developing different …

AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations

ZW Tan, E Guarnera, WV Tee… - Nucleic acids …, 2020 - academic.oup.com
The AlloSigMA 2 server provides an interactive platform for exploring the allosteric signaling
caused by ligand binding and/or mutations, for analyzing the allosteric effects of mutations …