Accurate prediction of protein structures and interactions using a three-track neural network

M Baek, F DiMaio, I Anishchenko, J Dauparas… - Science, 2021 - science.org
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of
Structure Prediction (CASP14) conference. We explored network architectures that …

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 …

Protein–protein interaction prediction methods: from docking-based to AI-based approaches

Y Tsuchiya, Y Yamamori, K Tomii - Biophysical Reviews, 2022 - Springer
Abstract Protein–protein interactions (PPIs), such as protein–protein inhibitor, antibody–
antigen complex, and supercomplexes play diverse and important roles in cells. Recent …

Critical assessment of methods of protein structure prediction (CASP)—Round XII

J Moult, K Fidelis, A Kryshtafovych… - Proteins: Structure …, 2018 - Wiley Online Library
This article reports the outcome of the 12th round of Critical Assessment of Structure
Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state …

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

MF Lensink, G Brysbaert, T Mauri… - Proteins: Structure …, 2021 - Wiley Online Library
We present the results for CAPRI Round 50, the fourth joint CASP‐CAPRI protein assembly
prediction challenge. The Round comprised a total of twelve targets, including six dimers …

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

MF Lensink, G Brysbaert, N Raouraoua… - Proteins: Structure …, 2023 - Wiley Online Library
We present the results for CAPRI Round 54, the 5th joint CASP‐CAPRI protein assembly
prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo …

CombFold: predicting structures of large protein assemblies using a combinatorial assembly algorithm and AlphaFold2

B Shor, D Schneidman-Duhovny - Nature methods, 2024 - nature.com
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein
structure prediction. However, large protein complexes are still challenging to predict due to …

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

J Liu, Z Guo, T Wu, RS Roy, F Quadir, C Chen… - Communications …, 2023 - nature.com
Abstract To enhance the AlphaFold-Multimer-based protein complex structure prediction, we
developed a quaternary structure prediction system (MULTICOM) to improve the input fed to …

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

MF Lensink, N Nadzirin, S Velankar… - Proteins: Structure …, 2020 - Wiley Online Library
We present the seventh report on the performance of methods for predicting the atomic
resolution structures of protein complexes offered as targets to the community‐wide initiative …

The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15

B Ozden, A Kryshtafovych… - … : Structure, Function, and …, 2023 - Wiley Online Library
In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The
community demonstrated exceptional performance in overall fold and interface contact …