Computational approaches to predict protein–protein interactions in crowded cellular environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

Computational prediction of protein–protein binding affinities

T Siebenmorgen, M Zacharias - Wiley Interdisciplinary Reviews …, 2020 - Wiley Online Library
Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …

Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation

RP Wurz, H Rui, K Dellamaggiore… - Nature …, 2023 - nature.com
Targeted protein degradation via “hijacking” of the ubiquitin-proteasome system using
proteolysis targeting chimeras (PROTACs) has evolved into a novel therapeutic modality …

The ClusPro web server for protein–protein docking

D Kozakov, DR Hall, B ** server that identifies binding hot spots of
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses …

F Chen, H Liu, H Sun, P Pan, Y Li, D Li… - Physical Chemistry …, 2016 - pubs.rsc.org
Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial
biological processes and even design compounds that interfere with PPIs with …

Performance and its limits in rigid body protein-protein docking

IT Desta, KA Porter, B **a, D Kozakov, S Vajda - Structure, 2020 - cell.com
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions
of complex conformations and thus revolutionized protein-protein docking. FFT-based …

[HTML][HTML] MANF regulates neuronal survival and UPR through its ER-located receptor IRE1α

V Kovaleva, LY Yu, L Ivanova, O Shpironok, J Nam… - Cell Reports, 2023 - cell.com
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum
(ER)-located protein with cytoprotective effects in neurons and pancreatic β cells in vitro and …

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

R Brenke, D Kozakov, GY Chuang, D Beglov… - …, 2009 - academic.oup.com
Motivation: The binding sites of proteins generally contain smaller regions that provide major
contributions to the binding free energy and hence are the prime targets in drug design …