[HTML][HTML] AlphaFold and implications for intrinsically disordered proteins

KM Ruff, RV Pappu - Journal of molecular biology, 2021 - Elsevier
Accurate predictions of the three-dimensional structures of proteins from their amino acid
sequences have come of age. AlphaFold, a deep learning-based approach to protein …

[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

Protein complex prediction with AlphaFold-Multimer

R Evans, M O'Neill, A Pritzel, N Antropova, A Senior… - biorxiv, 2021 - biorxiv.org
While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …

Disease variant prediction with deep generative models of evolutionary data

J Frazer, P Notin, M Dias, A Gomez, JK Min, K Brock… - Nature, 2021 - nature.com
Quantifying the pathogenicity of protein variants in human disease-related genes would
have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of …

Computed structures of core eukaryotic protein complexes

IR Humphreys, J Pei, M Baek, A Krishnakumar… - Science, 2021 - science.org
INTRODUCTION Protein-protein interactions play critical roles in biology, but the structures
of many eukaryotic protein complexes are unknown, and there are likely many interactions …

Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

R Yin, BY Feng, A Varshney, BG Pierce - Protein Science, 2022 - Wiley Online Library
High‐resolution experimental structural determination of protein–protein interactions has led
to valuable mechanistic insights, yet due to the massive number of interactions and …

Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness

F Obermeyer, M Jankowiak, N Barkas, SF Schaffner… - Science, 2022 - science.org
Repeated emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
variants with increased fitness underscores the value of rapid detection and characterization …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

Harnessing protein folding neural networks for peptide–protein docking

T Tsaban, JK Varga, O Avraham, Z Ben-Aharon… - Nature …, 2022 - nature.com
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2
and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we …

SWISS-MODEL: homology modelling of protein structures and complexes

A Waterhouse, M Bertoni, S Bienert… - Nucleic acids …, 2018 - academic.oup.com
Homology modelling has matured into an important technique in structural biology,
significantly contributing to narrowing the gap between known protein sequences and …