Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

C Geng, LC Xue, J Roel‐Touris… - Wiley Interdisciplinary …, 2019 - Wiley Online Library
Predicting the structure and thermodynamics of protein–protein interactions (PPIs) are key to
a proper understanding and modulation of their function. Since experimental methods might …

Recent advances in user-friendly computational tools to engineer protein function

CE Sequeiros-Borja, B Surpeta… - Briefings in …, 2021 - academic.oup.com
Progress in technology and algorithms throughout the past decade has transformed the field
of protein design and engineering. Computational approaches have become well-engrained …

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 …

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

X Liu, Y Luo, P Li, S Song, J Peng - PLoS computational biology, 2021 - journals.plos.org
Modeling the impact of amino acid mutations on protein-protein interaction plays a crucial
role in protein engineering and drug design. In this study, we develop GeoPPI, a novel …

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 …

Stereodivergent protein engineering of a lipase to access all possible stereoisomers of chiral esters with two stereocenters

J Xu, Y Cen, W Singh, J Fan, L Wu, X Lin… - Journal of the …, 2019 - ACS Publications
Enzymatic stereodivergent synthesis to access all possible product stereoisomers bearing
multiple stereocenters is relatively undeveloped, although enzymes are being increasingly …

Case report: A gain-of-function of hamartin may lead to a distinct “inverse TSC1-hamartin” phenotype characterized by reduced cell growth

AD Praticò, R Falsaperla, M Comella, G Belfiore… - Frontiers in …, 2023 - frontiersin.org
Mutations of TSC1 and TSC2 genes cause classical Tuberous Sclerosis Complex (TSC), a
neurocutaneous disorder characterized by a tendency to develop hamartias, hamartomas …

Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction

JJ Wee, K Xia - Briefings in Bioinformatics, 2022 - academic.oup.com
Protein–protein interactions (PPIs) play a significant role in nearly all cellular and biological
activities. Data-driven machine learning models have demonstrated great power in PPIs …

Mutation effect estimation on protein–protein interactions using deep contextualized representation learning

G Zhou, M Chen, CJT Ju, Z Wang… - NAR genomics and …, 2020 - academic.oup.com
The functional impact of protein mutations is reflected on the alteration of conformation and
thermodynamics of protein–protein interactions (PPIs). Quantifying the changes of two …

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

S Liu, T Zhu, M Ren, C Yu, D Bu… - Advances in Neural …, 2024 - proceedings.neurips.cc
Many crucial biological processes rely on networks of protein-protein interactions. Predicting
the effect of amino acid mutations on protein-protein binding is important in protein …