Leveraging transformers‐based language models in proteome bioinformatics

NQK Le - Proteomics, 2023 - Wiley Online Library
In recent years, the rapid growth of biological data has increased interest in using
bioinformatics to analyze and interpret this data. Proteomics, which studies the structure …

Deep learning tools to accelerate antibiotic discovery

A Cesaro, M Bagheri, M Torres, F Wan… - Expert Opinion on …, 2023 - Taylor & Francis
Introduction As machine learning (ML) and artificial intelligence (AI) expand to many
segments of our society, they are increasingly being used for drug discovery. Recent deep …

Artificial intelligence-driven antimicrobial peptide discovery

P Szymczak, E Szczurek - Current Opinion in Structural Biology, 2023 - Elsevier
Antimicrobial peptides (AMPs) emerge as promising agents against antimicrobial resistance,
providing an alternative to conventional antibiotics. Artificial intelligence (AI) revolutionized …

Machine learning for antimicrobial peptide identification and design

F Wan, F Wong, JJ Collins… - Nature Reviews …, 2024 - nature.com
Artificial intelligence (AI) and machine learning (ML) models are being deployed in many
domains of society and have recently reached the field of drug discovery. Given the …

Deep learning for advancing peptide drug development: Tools and methods in structure prediction and design

X Wu, H Lin, R Bai, H Duan - European Journal of Medicinal Chemistry, 2024 - Elsevier
Peptides can bind challenging disease targets with high affinity and specificity, offering
enormous opportunities for addressing unmet medical needs. However, peptides' unique …

iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model

W Xing, J Zhang, C Li, Y Huo… - Briefings in …, 2024 - academic.oup.com
As a kind of small molecule protein that can fight against various microorganisms in nature,
antimicrobial peptides (AMPs) play an indispensable role in maintaining the health of …

Diff-AMP: tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization

R Wang, T Wang, L Zhuo, J Wei, X Fu… - Briefings in …, 2024 - academic.oup.com
Antimicrobial peptides (AMPs), short peptides with diverse functions, effectively target and
combat various organisms. The widespread misuse of chemical antibiotics has led to …

Using the local symmetry in amino acids sequences of polypeptides to improve the predictive potential of models of their inhibitor activity

AP Toropova, AA Toropov - Amino Acids, 2023 - Springer
The minimal inhibitory concentrations (pMIC) are a valuable measure of the biological
activity of polypeptides. Numerical data on the pMIC are necessary to systematize …

[HTML][HTML] Classification of bioactive peptides: A systematic benchmark of models and encodings

E Bizzotto, G Zampieri, L Treu, P Filannino… - Computational and …, 2024 - Elsevier
Bioactive peptides are short amino acid chains possessing biological activity and exerting
physiological effects relevant to human health. Despite their therapeutic value, their …

Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity …

M Cui, M Wang, H Sun, L Yu, Z Su, X Zhang… - International Journal of …, 2024 - Elsevier
Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this
study was to mine, screen and characterize novel broad-spectrum bacteriocins from the …