Source code, test datasets and documentation are freely available for download at http:///www.github.com/jeffgauthier/pdpminer. This software is free and open source under the GNU General Public License v3.0.

Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of c...

This study by Alemany and Moore shows that Kip3/kinesin-8 requires the carboxy-terminal tail of beta-tubulin for depolymerase activity but not for binding

This study highlights that there is a broader diversity of enzymes with polyester depolymerase activity to be discovered from nature, beyond the well-known PETases. We demonstrate that uncharacterize...

Research on mitosis has predominantly examined cell-autonomous mechanisms, yet its regulation and consequences within the broader physiological context remain largely unexplored. It remains, therefore...

S0008621525002472

Cellular actin networks assemble by actin filament elongation at barbed ends and are thought to disa

Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, …

Klebsiella pneumoniae is an important pathogen, especially hypervirulent and multidrug-resistant K. pneumoniae, which are increasingly becoming a serious threat to global public health. Bacteriophages...

During mitosis, the human microtubule depolymerase KIF2C increases the turnover of kinetochore-micro

Bacteriophage isolation and characterization are important for advancing strategies to control bacterial growth, discovery of novel genes, such as biofilm depolymerase, and deploying phages as therape...

Catheter-related bloodstream infections (CRBSI) caused by drug-resistant Gram-negative bacteria remain a major clinical challenge. Here, a polydopamine-assisted depolymerase coating degrades bacteria....

Klebsiella pneumoniae Przondovirus KP32 presents a complex capsular degradation machinery comprised of two serotype-specific depolymerases, KP32gp38 a…

Background: Phage therapy shows promise for treating antibiotic-resistant Klebsiella infections. Identifying phage depolymerases that target Klebsiella capsular polysaccharides is crucial, as these capsules contribute to biofilm formation and virulence. However, homology-based searches have limitations in novel depolymerase discovery. Objective: To develop a machine learning model for identifying and ranking potential phage depolymerases targeting Klebsiella. Methods: We developed DepoRanker, a machine learning algorithm to rank proteins by their likelihood of being depolymerases. The model was experimentally validated on 5 newly characterized proteins and compared to BLAST. Results: DepoRanker demonstrated superior performance to BLAST in identifying potential depolymerases. Experimental validation confirmed its predictive ability on novel proteins. Conclusions: DepoRanker provides an accurate and functional tool to expedite depolymerase discovery for phage therapy against Klebsiella. It is available as a webserver and open-source software. Availability: Webserver: https://deporanker.dcs.warwick.ac.uk/ Source code: https://github.com/wgrgwrght/deporanker