Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

F Li, Y Wang, C Li, TT Marquez-Lago… - Briefings in …, 2019 - academic.oup.com
The roles of proteolytic cleavage have been intensively investigated and discussed during
the past two decades. This irreversible chemical process has been frequently reported to …

[HTML][HTML] Matrix metalloproteinases–From the cleavage data to the prediction tools and beyond

P Cieplak, AY Strongin - Biochimica et Biophysica Acta (BBA)-Molecular …, 2017 - Elsevier
Understanding the physiological role of any protease requires identification of both its
cleavage substrates and their relative cleavage efficacy as compared with other substrates …

Procleave: predicting protease-specific substrate cleavage sites by combining sequence and structural information

F Li, A Leier, Q Liu, Y Wang, D Xiang… - Genomics …, 2020 - academic.oup.com
Proteases are enzymes that cleave and hydrolyse the peptide bonds between two specific
amino acid residues of target substrate proteins. Protease-controlled proteolysis plays a key …

Predicting structural susceptibility of proteins to proteolytic processing

EV Matveev, VV Safronov, GV Ponomarev… - International Journal of …, 2023 - mdpi.com
The importance of 3D protein structure in proteolytic processing is well known. However,
despite the plethora of existing methods for predicting proteolytic sites, only a few of them …

[HTML][HTML] Permissive Conformations of a Transmembrane Helix Allow Intramembrane Proteolysis by γ-Secretase

M Ortner, N Guschtschin-Schmidt, W Stelzer… - Journal of Molecular …, 2023 - Elsevier
The intramembrane protease γ-secretase activates important signaling molecules, such as
Notch receptors. It is still unclear, however, how different elements within the primary …

Modulating hinge flexibility in the APP transmembrane domain alters γ-secretase cleavage

A Götz, N Mylonas, P Högel, M Silber, H Heinel… - Biophysical journal, 2019 - cell.com
Intramembrane cleavage of the β-amyloid precursor protein C99 substrate by γ-secretase is
implicated in Alzheimer's disease pathogenesis. Biophysical data have suggested that the N …

Cooperation of N-and C-terminal substrate transmembrane domain segments in intramembrane proteolysis by γ-secretase

NT Werner, P Högel, G Güner, W Stelzer… - Communications …, 2023 - nature.com
Intramembrane proteases play a pivotal role in biology and medicine, but how these
proteases decode cleavability of a substrate transmembrane (TM) domain remains unclear …

Predicting proteolysis in complex proteomes using deep learning

M Ozols, A Eckersley, CI Platt… - International journal of …, 2021 - mdpi.com
Both protease-and reactive oxygen species (ROS)-mediated proteolysis are thought to be
key effectors of tissue remodeling. We have previously shown that comparison of amino acid …

Helical stability of the GnTV transmembrane domain impacts on SPPL3 dependent cleavage

AA Papadopoulou, W Stelzer, M Silber, C Schlosser… - Scientific reports, 2022 - nature.com
Abstract Signal-Peptide Peptidase Like-3 (SPPL3) is an intramembrane cleaving aspartyl
protease that causes secretion of extracellular domains from type-II transmembrane …

CleavPredict: a platform for reasoning about matrix metalloproteinases proteolytic events

S Kumar, BI Ratnikov, MD Kazanov, JW Smith… - PLoS …, 2015 - journals.plos.org
CleavPredict (http://cleavpredict. sanfordburnham. org) is a Web server for substrate
cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational …