Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening.

The quest for effective virtual screening algorithms is hindered by the scarcity of training data, calling for innovative approaches. This study presents the use of experimental electron density (ED) data for improving active compound enrichment in virtual screening, supported by ED's ability to reflect the time-averaged behavior of ligands and solvents in the binding pocket. Experimental ED-based grid matching score (ExptGMS) was developed to score compounds by measuring the degree of matching between their binding conformations and a series of multi-resolution experimental ED grids.

G2GT: Retrosynthesis Prediction with Graph-to-Graph Attention Neural Network and Self-Training.

Retrosynthesis prediction, the task of identifying reactant molecules that can be used to synthesize product molecules, is a fundamental challenge in organic chemistry and related fields. To address this challenge, we propose a novel graph-to-graph transformation model, G2GT. The model is built on the standard transformer structure and utilizes graph encoders and decoders.

High-flexibility and high-accuracy phase delay calibration method for MEMS-based fringe projection systems.

Microelectromechanical system (MEMS) mirror based laser beam scanning (LBS) projectors for fringe projection profilometry (FPP) are becoming increasingly popular attributing to their small size and low cost. However, the initial phase of the scanning MEMS mirror employed in an LBS projector may vary over time, resulting in unstable and distorted fringe patterns. The distorted fringe patterns will largely decrease the accuracy of the three-dimensional (3D) topographic reconstruction.

A pocket-based 3D molecule generative model fueled by experimental electron density.

We report for the first time the use of experimental electron density (ED) as training data for the generation of drug-like three-dimensional molecules based on the structure of a target protein pocket. Similar to a structural biologist building molecules based on their ED, our model functions with two main components: a generative adversarial network (GAN) to generate the ligand ED in the input pocket and an ED interpretation module for molecule generation. The model was tested on three targets: a kinase (hematopoietic progenitor kinase 1), protease (SARS-CoV-2 main protease), and nuclear receptor (vitamin D receptor), and evaluated with a reference dataset composed of over 8000 compounds that have their activities reported in the literature.

Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein-Ligand Interaction Research.

We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling of noncovalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on reduced electron density gradient (RDG) theory describing intermolecular NCIs by ED and its first derivative. We established a database named Experimental NCI Database (ExptNCI; http://ncidatabase.

Knockdown of long non-coding RNA CCAT2 suppresses growth and metastasis of esophageal squamous cell carcinoma by inhibiting the -catenin/WISP1 signaling pathway.

Objective: Long non-coding RNA (lncRNA) colon cancer-associated transcript 2 (CCAT2) plays oncogenic roles in several cancers, including esophageal squamous cell carcinoma (ESCC). However, the specific mechanism of how CCAT2 influences ESCC tumorigenesis is still unknown.

Methods: Using RT-qPCR, the mRNA expression levels of CCAT2 in 33 paired ESCC and adjacent non-cancer tissues and cell lines were measured.

Parallel PWMs based fully digital transmitter with wide carrier frequency range.

The carrier-frequency (CF) and intermediate-frequency (IF) pulse-width modulators (PWMs) based on delay lines are proposed, where baseband signals are conveyed by both positions and pulse widths or densities of the carrier clock. By combining IF-PWM and precorrected CF-PWM, a fully digital transmitter with unit-delay autocalibration is implemented in 180 nm CMOS for high reconfiguration. The proposed architecture achieves wide CF range of 2 M-1 GHz, high power efficiency of 70%, and low error vector magnitude (EVM) of 3%, with spectrum purity of 20 dB optimized in comparison to the existing designs.