iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

J Song, Y Wang, F Li, T Akutsu… - Briefings in …, 2019 - academic.oup.com
Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The
key to better understanding the mechanisms that control this process is to identify the …

[HTML][HTML] Calpains—An elaborate proteolytic system

Y Ono, H Sorimachi - Biochimica et Biophysica Acta (BBA)-Proteins and …, 2012 - Elsevier
Calpain is an intracellular Ca2+-dependent cysteine protease (EC 3.4. 22.17; Clan CA,
family C02). Recent expansion of sequence data across the species definitively shows that …

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites

J Song, H Tan, AJ Perry, T Akutsu, GI Webb… - PloS one, 2012 - journals.plos.org
The ability to catalytically cleave protein substrates after synthesis is fundamental for all
forms of life. Accordingly, site-specific proteolysis is one of the most important post …

Caspase substrates and cellular remodeling

ED Crawford, JA Wells - Annual review of biochemistry, 2011 - annualreviews.org
The caspases are unique proteases that mediate the major morphological changes of
apoptosis and various other cellular remodeling processes. As we catalog and study the …

Caspase substrates

JC Timmer, GS Salvesen - Cell Death & Differentiation, 2007 - nature.com
The relatively common occurrence of sequences within proteins that match the consensus
substrate specificity of caspases in intracellular proteins suggests a multitude of substrates …

Noncytotoxic Lytic Granule–Mediated CD8+ T Cell Inhibition of HSV-1 Reactivation from Neuronal Latency

JE Knickelbein, KM Khanna, MB Yee, CJ Baty… - Science, 2008 - science.org
Reactivation of herpes simplex virus type 1 (HSV-1) from neuronal latency is a common and
potentially devastating cause of disease worldwide. CD8+ T cells can completely inhibit …

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy

J Song, F Li, A Leier, TT Marquez-Lago, T Akutsu… - …, 2018 - academic.oup.com
Proteases are enzymes that specifically cleave the peptide backbone of their target proteins.
As an important type of irreversible post-translational modification, protein cleavage …

GeneTrail—advanced gene set enrichment analysis

C Backes, A Keller, J Kuentzer, B Kneissl… - Nucleic acids …, 2007 - academic.oup.com
We present a comprehensive and efficient gene set analysis tool, called 'GeneTrail'that
offers a rich functionality and is easy to use. Our web-based application facilitates the …

Macrophage activation and polarization modify P2X7 receptor secretome influencing the inflammatory process

C de Torre-Minguela, M Barberà-Cremades… - Scientific reports, 2016 - nature.com
The activation of P2X7 receptor (P2X7R) on M1 polarized macrophages induces the
assembly of the NLRP3 inflammasome leading to the release of pro-inflammatory cytokines …

The linear ubiquitin chain assembly complex regulates TRAIL‐induced gene activation and cell death

E Lafont, C Kantari‐Mimoun, P Draber… - The EMBO …, 2017 - embopress.org
The linear ubiquitin chain assembly complex (LUBAC) is the only known E3 ubiquitin ligase
which catalyses the generation of linear ubiquitin linkages de novo. LUBAC is a crucial …