AlphaCutter: Efficient removal of non-globular regions from predicted protein structures.

A huge number of high-quality predicted protein structures are now publicly available. However, many of these structures contain non-globular regions, which diminish the performance of downstream structural bioinformatic applications. In this study, we develop AlphaCutter for the removal of non-globular regions from predicted protein structures.

NbX: Machine Learning-Guided Re-Ranking of Nanobody-Antigen Binding Poses.

Modeling the binding pose of an antibody is a prerequisite to structure-based affinity maturation and design. Without knowing a reliable binding pose, the subsequent structural simulation is largely futile. In this study, we have developed a method of machine learning-guided re-ranking of antigen binding poses of nanobodies, the single-domain antibody which has drawn much interest recently in antibody drug development.

FPredX: Interpretable models for the prediction of spectral maxima, brightness, and oligomeric states of fluorescent proteins.

Fluorescent protein (FP) design is among the challenging protein design problems due to the tradeoffs among multiple properties to be optimized. Despite the accumulated efforts in design and characterization, progress has been slow in gaining a full understanding of sequence-property relationships to tackle the multiobjective design problem in FPs. In this study, we approach this problem by developing FPredX, a collection of gradient-boosted decision tree models, which mapped FP sequences to four major design targets of FPs, including excitation maximum, emission maximum, brightness, and oligomeric state.

Coptisine-induced inhibition of Helicobacter pylori: elucidation of specific mechanisms by probing urease active site and its maturation process.

In this study, we examined the anti-Helicobactor pylori effects of the main protoberberine-type alkaloids in Rhizoma Coptidis. Coptisine exerted varying antibacterial and bactericidal effects against three standard H. pylori strains and eleven clinical isolates, including four drug-resistant strains, with minimum inhibitory concentrations ranging from 25 to 50 μg/mL and minimal bactericidal concentrations ranging from 37.