MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.

Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction datasets are urgently needed for large language models. To address this, we present MISATO, a dataset that combines quantum mechanical properties of small molecules and associated molecular dynamics simulations of ~20,000 experimental protein-ligand complexes with extensive validation of experimental data.

Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration.

CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically investigating factors influencing guide depletion in genome-wide essentiality screens, with the surprising discovery that gene-specific features substantially impact prediction. We develop a mixed-effect random forest regression model that provides better estimates of guide efficiency.

New clues on carcinogenicity-related substructures derived from mining two large datasets of chemical compounds.

In this study, new molecular fragments associated with genotoxic and nongenotoxic carcinogens are introduced to estimate the carcinogenic potential of compounds. Two rule-based carcinogenesis models were developed with the aid of SARpy: model R (from rodents' experimental data) and model E (from human carcinogenicity data). Structural alert extraction method of SARpy uses a completely automated and unbiased manner with statistical significance.

Fluorimetric detection of boron by azomethine-H in micellar solution and sol-gel.

Mixtures of boron and azomethine-H in solution result in slow complexation. Addition of sodium dodecyl sulfate (SDS), polyethylene glycol dodecyl ether (Brij-35), 4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol (TritonX-100), and cetyltrimethyl ammonium bromide (CTAB) result in considerable decrease in complexation time and enhancement in signal of peak in solution and also sol-gel. The fluorescence of the complex is monitored at an emission wavelength of 486 nm with excitation at 416 nm.