A structural biology community assessment of AlphaFold2 applications
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …
biological processes of the cell. Recent developments in computational methods for protein …
Deep learning for protein structure prediction and design—progress and applications
J Jänes, P Beltrao - Molecular Systems Biology, 2024 - embopress.org
Proteins are the key molecular machines that orchestrate all biological processes of the cell.
Most proteins fold into three-dimensional shapes that are critical for their function. Studying …
Most proteins fold into three-dimensional shapes that are critical for their function. Studying …
Short linear motifs in colorectal cancer interactome and tumorigenesis
C Fasano, V Grossi, G Forte, C Simone - Cells, 2022 - mdpi.com
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for
cancer initiation, progression, and invasion. This multistage process is based on a dense …
cancer initiation, progression, and invasion. This multistage process is based on a dense …
CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation
C Wei, L Jia, X Huang, J Tan, M Wang, J Niu, Y Hou… - Cell Research, 2022 - nature.com
Chromatin is spatially organized into three-dimensional structures at different levels
including A/B compartments, topologically associating domains and loops. The canonical …
including A/B compartments, topologically associating domains and loops. The canonical …
Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14)
An evolutionary‐based definition and classification of target evaluation units (EUs) is
presented for the 14th round of the critical assessment of structure prediction (CASP14) …
presented for the 14th round of the critical assessment of structure prediction (CASP14) …
[HTML][HTML] Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome
Carboxysomes are proteinaceous bacterial microcompartments that sequester the key
enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a …
enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a …
[HTML][HTML] SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer
W Hu, M Ohue - Computational and Structural Biotechnology Journal, 2024 - Elsevier
Rapid advancements in protein sequencing technology have resulted in gaps between
proteins with identified sequences and those with mapped structures. Although sequence …
proteins with identified sequences and those with mapped structures. Although sequence …
Limits and potential of combined folding and docking
Motivation In the last decade, de novo protein structure prediction accuracy for individual
proteins has improved significantly by utilising deep learning (DL) methods for harvesting …
proteins has improved significantly by utilising deep learning (DL) methods for harvesting …
Deep learning in modeling protein complex structures: From contact prediction to end-to-end approaches
Protein–protein interactions play crucial roles in many biological processes. Traditionally,
protein complex structures are normally built by protein–protein docking. With the rapid …
protein complex structures are normally built by protein–protein docking. With the rapid …
[HTML][HTML] Extending the horizon of homology detection with coevolution-based structure prediction
Traditional sequence analysis algorithms fail to identify distant homologies when they lie
beyond a detection horizon. In this review, we discuss how co-evolution-based contact and …
beyond a detection horizon. In this review, we discuss how co-evolution-based contact and …