Plant antimicrobial peptides: state of the art, in silico prediction and perspectives in the omics era

CA Santos-Silva, L Zupin… - … and Biology Insights, 2020 - journals.sagepub.com
Even before the perception or interaction with pathogens, plants rely on constitutively
guardian molecules, often specific to tissue or stage, with further expression after contact …

Bioinformatic prediction of plant–pathogenicity effector proteins of fungi

DAB Jones, S Bertazzoni, CJ Turo, RA Syme… - Current Opinion in …, 2018 - Elsevier
Highlights•Review of current methods in fungal plant pathogenicity effector protein
prediction.•Recent advances have been made in structural and machine learning-based …

KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling

G Postic, J Gracy, C Périn, L Chiche… - Nucleic Acids …, 2018 - academic.oup.com
Knottins, or inhibitor cystine knots (ICKs), are ultra-stable miniproteins with multiple
applications in drug design and medical imaging. These widespread and functionally …

Current and prospective computational approaches and challenges for develo** COVID-19 vaccines

W Hwang, W Lei, NM Katritsis, M MacMahon… - Advanced drug delivery …, 2021 - Elsevier
Abstract SARS-CoV-2, which causes COVID-19, was first identified in humans in late 2019
and is a coronavirus which is zoonotic in origin. As it spread around the world there has …

AB-Amy: machine learning aided amyloidogenic risk prediction of therapeutic antibody light chains

Y Zhou, Z Huang, Y Gou, S Liu, W Yang… - Antibody …, 2023 - academic.oup.com
Over 120 FDA-approved antibody-based therapeutics are used to treat a variety of diseases.
However, many candidates could fail because of unfavorable physicochemical properties …

Supercomputing leverages quantum machine learning and Grover's algorithm

B Khanal, J Orduz, P Rivas, E Baker - The Journal of Supercomputing, 2023 - Springer
The complexity of searching algorithms in classical computing is a classic problem and a
research area. Quantum computers and quantum algorithms can efficiently compute some …

Application of kNN and SVM to predict the prognosis of advanced schistosomiasis

X Zhou, H Wang, C Xu, L Peng, F Xu, L Lian… - Parasitology …, 2022 - Springer
Predictive models for prognosis of small sample advanced schistosomiasis patients have
not been well studied. We aimed to construct prognostic predictive models of small sample …

Protein classification using modified n-grams and skip-grams

SMA Islam, BJ Heil, CM Kearney, EJ Baker - Bioinformatics, 2018 - academic.oup.com
Motivation Classification by supervised machine learning greatly facilitates the annotation of
protein characteristics from their primary sequence. However, the feature generation step in …

Multiple Classes of Antimicrobial Peptides in Amaranthus tricolor Revealed by Prediction, Proteomics, and Mass Spectrometric Characterization

TB Moyer, JL Allen, LN Shaw… - Journal of natural products, 2021 - ACS Publications
Traditional medicinal plants are rich reservoirs of antimicrobial agents, including
antimicrobial peptides (AMPs). Advances in genomic sequencing, in silico AMP predictions …

Making plants into cost-effective bioreactors for highly active antimicrobial peptides

M Ghidey, SMA Islam, G Pruett, CM Kearney - New Biotechnology, 2020 - Elsevier
As antibiotic-resistant bacterial pathogens become an ever-increasing concern,
antimicrobial peptides (AMPs) have grown increasingly attractive as alternatives. Potentially …