Machine learning methods for small data challenges in molecular science

B Dou, Z Zhu, E Merkurjev, L Ke, L Chen… - Chemical …, 2023 - ACS Publications
Small data are often used in scientific and engineering research due to the presence of
various constraints, such as time, cost, ethics, privacy, security, and technical limitations in …

Antimicrobial peptides: an update on classifications and databases

A Bin Hafeez, X Jiang, PJ Bergen, Y Zhu - International journal of …, 2021 - mdpi.com
Antimicrobial peptides (AMPs) are distributed across all kingdoms of life and are an
indispensable component of host defenses. They consist of predominantly short cationic …

Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii

G Liu, DB Catacutan, K Rathod, K Swanson… - Nature Chemical …, 2023 - nature.com
Acinetobacter baumannii is a nosocomial Gram-negative pathogen that often displays
multidrug resistance. Discovering new antibiotics against A. baumannii has proven …

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

D Kuznetsov, F Tegenfeldt, M Manni… - Nucleic Acids …, 2023 - academic.oup.com
OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of
eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of …

Enzyme function prediction using contrastive learning

T Yu, H Cui, JC Li, Y Luo, G Jiang, H Zhao - Science, 2023 - science.org
Enzyme function annotation is a fundamental challenge, and numerous computational tools
have been developed. However, most of these tools cannot accurately predict functional …

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

M Baek, R McHugh, I Anishchenko, H Jiang, D Baker… - Nature …, 2024 - nature.com
Protein–RNA and protein–DNA complexes play critical roles in biology. Despite
considerable recent advances in protein structure prediction, the prediction of the structures …

[HTML][HTML] Multiple early factors anticipate post-acute COVID-19 sequelae

Y Su, D Yuan, DG Chen, RH Ng, K Wang, J Choi, S Li… - Cell, 2022 - cell.com
Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However,
quantifiable risk factors for PASC and their biological associations are poorly resolved. We …

Predicting multiple conformations via sequence clustering and AlphaFold2

HK Wayment-Steele, A Ojoawo, R Otten, JM Apitz… - Nature, 2024 - nature.com
Abstract AlphaFold2 (ref.) has revolutionized structural biology by accurately predicting
single structures of proteins. However, a protein's biological function often depends on …

Ancient gene linkages support ctenophores as sister to other animals

DT Schultz, SHD Haddock, JV Bredeson, RE Green… - Nature, 2023 - nature.com
A central question in evolutionary biology is whether sponges or ctenophores (comb jellies)
are the sister group to all other animals. These alternative phylogenetic hypotheses imply …

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

A Heinken, J Hertel, G Acharya, DA Ravcheev… - Nature …, 2023 - nature.com
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …