A comprehensive review of the recent advances on predicting drug-target affinity based on deep learning

X Zeng, SJ Li, SQ Lv, ML Wen, Y Li - Frontiers in Pharmacology, 2024 - frontiersin.org
Accurate calculation of drug-target affinity (DTA) is crucial for various applications in the
pharmaceutical industry, including drug screening, design, and repurposing. However …

ATP-Triggered Fe(CN)2CO Synthon Transfer from the Maturase HypCD to the Active Site of Apo-[NiFe]-Hydrogenase

A Kwiatkowski, G Caserta, AC Schulz… - Journal of the …, 2024 - ACS Publications
[NiFe]-hydrogenases catalyze the reversible activation of H2 using a unique NiFe (CN) 2CO
metal site, which is assembled by a sophisticated multiprotein machinery. The [4Fe–4S] …

LazyAF, a pipeline for accessible medium-scale in silico prediction of protein-protein interactions

TC McLean - Microbiology, 2024 - microbiologyresearch.org
Artificial intelligence has revolutionized the field of protein structure prediction. However,
with more powerful and complex software being developed, it is accessibility and ease of …

Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning

X Zeng, GP Su, SJ Li, SQ Lv, ML Wen, Y Li - BMC bioinformatics, 2024 - Springer
Background Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding
sites (DTS) is crucial for drug screening, repositioning, and design, as well as for …

The developmental transcription factor TBX3 physically engages with the Wnt/β-catenin transcriptional complex in human colorectal cancer cells to regulate …

A Jauregi-Miguel, S Soderholm, TL Weiss, A Nordin… - bioRxiv, 2023 - biorxiv.org
Wnt signaling orchestrates gene expression in a plethora of processes during development
and adult cell homeostasis via the action of nuclear β-catenin. Furthermore, neoplasia of the …

[HTML][HTML] Discovering Intron Gain Events in Humans through Large-Scale Evolutionary Comparisons

C Hoh, SL Salzberg - bioRxiv, 2024 - ncbi.nlm.nih.gov
The rapid growth in the number of sequenced genomes makes it possible to search for the
appearance of entirely new introns in the human lineage. In this study, we compared the …

Exploring structure-function relationships in engineered receptor performance using computational structure prediction

WK Corcoran, A Cosio, HI Edelstein, JN Leonard - bioRxiv, 2024 - biorxiv.org
Engineered receptors play increasingly important roles in transformative cell-based
therapies. However, the structural mechanisms that drive differences in performance across …

Adaptive protein coevolution preserves telomere integrity

H Futeran, SY Lin, MT Levine - bioRxiv, 2024 - biorxiv.org
Many essential conserved functions depend, paradoxically, on proteins that evolve rapidly
under positive selection. How such adaptively evolving proteins promote biological …

PEX39 facilitates the peroxisomal import of PTS2 proteins

WW Chen, TA Rodrigues, D Wendscheck, AG Pedrosa… - bioRxiv, 2024 - biorxiv.org
Peroxisomes are metabolic organelles essential for human health. Defects in peroxisomal
biogenesis proteins (peroxins/PEXs) cause devastating disease. PEX7 binds newly …

PySSA: end-user protein structure prediction and visual analysis with ColabFold and PyMOL

H Kullik, M Urban, J Schaub, A Loidl-Stahlhofen… - 2024 - chemrxiv.org
Computational methods for the accurate prediction of protein folding based on amino acid
sequences have been researched for decades. The field has been significantly advanced in …