Accelerating antibiotic discovery through artificial intelligence

MCR Melo, JRMA Maasch… - Communications …, 2021 - nature.com
By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the
host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics …

[HTML][HTML] Matrikines as mediators of tissue remodelling

N Jariwala, M Ozols, M Bell, E Bradley… - Advanced drug delivery …, 2022 - Elsevier
Extracellular matrix (ECM) proteins confer biomechanical properties, maintain cell
phenotype and mediate tissue repair (via release of sequestered cytokines and proteases) …

Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning

JRMA Maasch, MDT Torres, MCR Melo… - Cell Host & Microbe, 2023 - cell.com
Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive
molecules that are no longer encoded by extant organisms. To prospect for antimicrobial …

iProt-Sub: a comprehensive package for accurately map** 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 …

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 …

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

F Li, J Chen, A Leier, T Marquez-Lago, Q Liu… - …, 2020 - academic.oup.com
Motivation Proteases are enzymes that cleave target substrate proteins by catalyzing the
hydrolysis of peptide bonds between specific amino acids. While the functional proteolysis …

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 …

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

F Li, A Leier, Q Liu, Y Wang, D **ang… - 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 …

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 …

Prediction and design of protease enzyme specificity using a structure-aware graph convolutional network

C Lu, JH Lubin, VV Sarma, SZ Stentz, G Wang… - Proceedings of the …, 2023 - pnas.org
Site-specific proteolysis by the enzymatic cleavage of small linear sequence motifs is a key
posttranslational modification involved in physiology and disease. The ability to robustly and …