Critical assessment of methods for predicting the 3D structure of proteins and protein complexes
SJ Wodak, S Vajda, MF Lensink… - Annual review of …, 2023 - annualreviews.org
Advances in a scientific discipline are often measured by small, incremental steps. In this
review, we report on two intertwined disciplines in the protein structure prediction field …
review, we report on two intertwined disciplines in the protein structure prediction field …
PROTAC technology: A new drug design for chemical biology with many challenges in drug discovery
N Guedeney, M Cornu, F Schwalen, C Kieffer… - Drug Discovery …, 2023 - Elsevier
Abstract Target Protein Degradation TPD is a new avenue and revolutionary for therapeutics
because redefining the principles of classical drug discovery and guided by event-based …
because redefining the principles of classical drug discovery and guided by event-based …
Learning from protein structure with geometric vector perceptrons
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine
learning, but there has yet to emerge a unifying network architecture that simultaneously …
learning, but there has yet to emerge a unifying network architecture that simultaneously …
QMEANDisCo—distance constraints applied on model quality estimation
G Studer, C Rempfer, AM Waterhouse… - …, 2020 - academic.oup.com
Motivation Methods that estimate the quality of a 3D protein structure model in absence of an
experimental reference structure are crucial to determine a model's utility and potential …
experimental reference structure are crucial to determine a model's utility and potential …
PROTAC-DB 2.0: an updated database of PROTACs
Proteolysis targeting chimeras (PROTACs), which harness the ubiquitin-proteasome system
to selectively induce targeted protein degradation, represent an emerging therapeutic …
to selectively induce targeted protein degradation, represent an emerging therapeutic …
In situ architecture of the ER–mitochondria encounter structure
The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane
biogenesis that rely on lipid exchange via membrane contact sites,–, but the underpinning …
biogenesis that rely on lipid exchange via membrane contact sites,–, but the underpinning …
[HTML][HTML] Improved protein structure refinement guided by deep learning based accuracy estimation
We develop a deep learning framework (DeepAccNet) that estimates per-residue accuracy
and residue-residue distance signed error in protein models and uses these predictions to …
and residue-residue distance signed error in protein models and uses these predictions to …
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 …
prediction challenge. The Round comprised a total of twelve targets, including six dimers …
Integrative modeling of PROTAC-mediated ternary complexes
Proteolysis-targeting chimeras (PROTACs), which selectively induce targeted protein
degradation, represent an emerging drug discovery technology. Although numerous …
degradation, represent an emerging drug discovery technology. Although numerous …
IntFOLD: an integrated web resource for high performance protein structure and function prediction
The IntFOLD server provides a unified resource for the automated prediction of: protein
tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain …
tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain …