DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces

M Réau, N Renaud, LC Xue, AMJJ Bonvin - Bioinformatics, 2023 - academic.oup.com
Motivation Gaining structural insights into the protein–protein interactome is essential to
understand biological phenomena and extract knowledge for rational drug design or protein …

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

N Renaud, C Geng, S Georgievska… - Nature …, 2021 - nature.com
Abstract Three-dimensional (3D) structures of protein complexes provide fundamental
information to decipher biological processes at the molecular scale. The vast amount of …

[HTML][HTML] Modeling and structure determination of homo-oligomeric proteins: An overview of challenges and current approaches

A Gaber, M Pavšič - International journal of molecular sciences, 2021 - mdpi.com
Protein homo-oligomerization is a very common phenomenon, and approximately half of
proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority …

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

G Capitani, JM Duarte, K Baskaran, S Bliven… - …, 2016 - academic.oup.com
Modern structural biology still draws the vast majority of information from crystallography, a
technique where the objects being investigated are embedded in a crystal lattice. Given the …

The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

MF Lensink, S Velankar, M Baek, L Heo… - Proteins: Structure …, 2018 - Wiley Online Library
We present the quality assessment of 5613 models submitted by predictor groups from both
CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP …

Synthetic peptides that antagonize the angiotensin-converting enzyme-2 (ACE-2) interaction with SARS-CoV-2 receptor binding spike protein

A Sadremomtaz, ZM Al-Dahmani… - Journal of medicinal …, 2021 - ACS Publications
The SARS-CoV-2 viral spike protein S receptor-binding domain (S-RBD) binds ACE2 on
host cells to initiate molecular events, resulting in intracellular release of the viral genome …

Mutations in SULT2B1 cause autosomal-recessive congenital ichthyosis in humans

L Heinz, GJ Kim, S Marrakchi, J Christiansen… - The American Journal of …, 2017 - cell.com
Ichthyoses are a clinically and genetically heterogeneous group of genodermatoses
associated with abnormal scaling of the skin over the whole body. Mutations in nine genes …

Automated evaluation of quaternary structures from protein crystals

S Bliven, A Lafita, A Parker, G Capitani… - PLoS computational …, 2018 - journals.plos.org
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to
understanding their function, physico-chemical properties and mode of interaction with other …

PDB-wide identification of biological assemblies from conserved quaternary structure geometry

S Dey, DW Ritchie, ED Levy - Nature methods, 2018 - nature.com
Protein structures are key to understanding biomolecular mechanisms and diseases, yet
their interpretation is hampered by limited knowledge of their biologically relevant …

Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction

Y Yue, S Li, Y Cheng, L Wang, T Hou, Z Zhu… - Nature …, 2024 - nature.com
Abstract Structure-based machine learning algorithms have been utilized to predict the
properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is …