The trRosetta server for fast and accurate protein structure prediction

Z Du, H Su, W Wang, L Ye, H Wei, Z Peng… - Nature protocols, 2021 - nature.com
The trRosetta (transform-restrained Rosetta) server is a web-based platform for fast and
accurate protein structure prediction, powered by deep learning and Rosetta. With the input …

Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms

DE Gordon, J Hiatt, M Bouhaddou, VV Rezelj, S Ulferts… - Science, 2020 - science.org
INTRODUCTION The emergence of three lethal coronaviruses in< 20 years and the urgency
of the COVID-19 pandemic have prompted efforts to develop new therapeutic strategies …

Independent se (3)-equivariant models for end-to-end rigid protein docking

OE Ganea, X Huang, C Bunne, Y Bian… - arXiv preprint arXiv …, 2021 - arxiv.org
Protein complex formation is a central problem in biology, being involved in most of the cell's
processes, and essential for applications, eg drug design or protein engineering. We tackle …

Cryo-EM structure of a type IV secretion system

K Macé, AK Vadakkepat, A Redzej, N Lukoyanova… - Nature, 2022 - nature.com
Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often
plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which …

xTrimoPGLM: unified 100B-scale pre-trained transformer for deciphering the language of protein

B Chen, X Cheng, P Li, Y Geng, J Gong, S Li… - arXiv preprint arXiv …, 2024 - arxiv.org
Protein language models have shown remarkable success in learning biological information
from protein sequences. However, most existing models are limited by either autoencoding …

Molecular mechanism of evolution and human infection with SARS-CoV-2

J He, H Tao, Y Yan, SY Huang, Y Xiao - Viruses, 2020 - mdpi.com
The outbreak of a novel coronavirus, which was later formally named the severe acute
respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis …

The lipoprotein-associated phospholipase A2 inhibitor Darapladib sensitises cancer cells to ferroptosis by remodelling lipid metabolism

M Oh, SY Jang, JY Lee, JW Kim, Y Jung, J Kim… - Nature …, 2023 - nature.com
Arachidonic and adrenic acids in the membrane play key roles in ferroptosis. Here, we
reveal that lipoprotein-associated phospholipase A2 (Lp-PLA2) controls intracellular …

Aligned diffusion Schrödinger bridges

VR Somnath, M Pariset, YP Hsieh… - Uncertainty in …, 2023 - proceedings.mlr.press
Diffusion Schrödinger bridges (DSBs) have recently emerged as a powerful framework for
recovering stochastic dynamics via their marginal observations at different time points …

Integrated structure prediction of protein–protein docking with experimental restraints using ColabDock

S Feng, Z Chen, C Zhang, Y Xie… - Nature Machine …, 2024 - nature.com
Protein complex structure prediction plays important roles in various applications, such as
drug discovery and antibody design. However, due to limited prediction accuracy, there are …