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The development of nonpyrolytic catalysts featuring precisely defined active sites represents an effective strategy for investigating the fundamental relationship between the catalytic activity of oxygen reduction reaction (ORR) catalysts and their local coordination environments. In this study, we have synthesized a series of model electrocatalysts with well‐defined CoN4 centers and nonplanar symmetric coordination structures. These catalysts were prepared by a sequential process involving the chelation of cobalt salts and 1,10‐phenanthroline‐based ligands with various substituent groups (phen(X), where X=OH, CH3, H, Br, Cl) onto covalent triazine frameworks (CTFs). By modulating the electron‐donating or electron‐withdrawing properties of the substituent groups on the phen‐based ligands, the electron density surrounding the CoN4 centers was effectively controlled. Our results demonstrated a direct correlation between the catalytic activity of the CoN4 centers and the electron‐donating ability of the substituent group on the phenanthroline ligands. Notably, the catalyst denoted as BCTF−Co‐phen(OH), featuring the electron‐donating OH group, exhibited the highest ORR catalytic activity. This custom‐crafted catalyst achieved a remarkable half‐wave potential of up to 0.80 V vs. RHE and an impressive turnover frequency (TOF) value of 47.4×10−3 Hz at 0.80 V vs. RHE in an alkaline environment. [ABSTRACT FROM AUTHOR]

The 'pseudokinase' SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome.

Imbalanced domain prediction analysis is currently one of the hot research topics. Many real‐world data mining analyses involve using imbalanced data to obtain predictive models. In the context of imbalance, research on classification problems has been extensive, but research on regression problems is negligible. Rare values rarely occur in imbalanced regression problems, but the focus is on accurately predicting the continuous target variables of rare instances. One of the challenges in imbalanced regression is finding a suitable strategy to rebalance the original dataset in order to improve the predictive performance of the model in rare instances. In this study, two algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS). ACOS rebalances the original dataset by generating new instances through the affine combinations of the original examples. The region where the new instances are generated can be adjusted based on the distribution of the data, ensuring that the generated cases better mimic the distribution of the original examples. The comparison among ACOS, SNOCCR, and other preprocessing methods was conducted on 15 datasets to validate the predictive performance of models trained on rebalanced datasets for rare instances. The experimental results indicate that ACOS outperforms other existing methods. In this study, two over‐sampling algorithms are proposed: sigma nearest over‐sampling based on convex combination for regression (SNOCCR) and affine combination‐based over‐sampling (ACOS) in order to improve the predictive performance of the model in imbalanced regression. The experimental results indicate that ACOS outperforms other existing methods. [ABSTRACT FROM AUTHOR]

Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. We have therefore created an expert system, DOCK Blaster, to investigate the feasibility of full automation. The method requires a PDB code, sometimes with a ligand structure, and from that alone can launch a full screen of large libraries. A critical feature is self-assessment, which estimates the anticipated reliability of the automated screening results using pose fidelity and enrichment. Against common benchmarks, DOCK Blaster recapitulates the crystal ligand pose within 2 A rmsd 50-60% of the time; inferior to an expert, but respectrable. Half the time the ligand also ranked among the top 5% of 100 physically matched decoys chosen on the fly. Further tests were undertaken culminating in a study of 7755 eligible PDB structures. In 1398 cases, the redocked ligand ranked in the top 5% of 100 property-matched decoys while also posing within 2 A rmsd, suggesting that unsupervised prospective docking is viable. DOCK Blaster is available at http://blaster.docking.org .