GSScore: a novel Graphormer-based shell-like scoring method for protein-ligand docking.

Protein-ligand interactions (PLIs) are essential for cellular activities and drug discovery. But due to the complexity and high cost of experimental methods, there is a great demand for computational approaches to recognize PLI patterns, such as protein-ligand docking. In recent years, more and more models based on machine learning have been developed to directly predict the root mean square deviation (RMSD) of a ligand docking pose with reference to its native binding pose.

Distribution patterns and drivers of urban green space and plant diversity in Haikou, China.

Investigating historical and ongoing changes in urban green space (UGS) and urban plant diversity (UPD) provides critical insights into urban ecology and urban planning development. The present study illuminates some of the transformations which can occur in rapidly developing urban landscapes. In this work, we used 30 m resolution images from the Landsat 5 satellite from 2015 to investigate UGS patterns in Haikou City, China.

ViTScore: A Novel Three-Dimensional Vision Transformer Method for Accurate Prediction of Protein-Ligand Docking Poses.

Protein-ligand interactions (PLIs) are essential for cellular activities and drug discovery, and due to the complexity and high cost of experimental methods, there is a great demand for computational approaches, such as protein-ligand docking, to decipher PLI patterns. One of the most challenging aspects of protein-ligand docking is to identify near-native conformations from a set of poses, but traditional scoring functions still have limited accuracy. Therefore, new scoring methods are urgently needed for methodological and/or practical implications.

Spatiotemporal Variation of Urban Plant Diversity and above Ground Biomass in Haikou, China.

Understanding the drivers of urban plant diversity (UPD) and above ground biomass (AGB) in urbanized areas is critical for urban ecosystem services and biodiversity protection. The relationships between UPD and AGB have been investigated simultaneously. However, the drivers of UPD and AGB have been explored independently in tropical coastal areas at different time points.

TRScore: a 3D RepVGG-based scoring method for ranking protein docking models.

Motivation: Protein-protein interactions (PPI) play important roles in cellular activities. Due to the technical difficulty and high cost of experimental methods, there are considerable interests towards the development of computational approaches, such as protein docking, to decipher PPI patterns. One of the important and difficult aspects in protein docking is recognizing near-native conformations from a set of decoys, but unfortunately, traditional scoring functions still suffer from limited accuracy.

Complete plastome sequence of (Roxb.) Esser (Euphorbiaceae).

belongs to the family Euphorbiaceae and is distributed in Yunnan province, China, and other southeast Asian countries, e.g., Bangladesh, Cambodia, India, Indonesia, etc.

MHC2SKpan: a novel kernel based approach for pan-specific MHC class II peptide binding prediction.

Background: Computational methods for the prediction of Major Histocompatibility Complex (MHC) class II binding peptides play an important role in facilitating the understanding of immune recognition and the process of epitope discovery. To develop an effective computational method, we need to consider two important characteristics of the problem: (1) the length of binding peptides is highly flexible; and (2) MHC molecules are extremely polymorphic and for the vast majority of them there are no sufficient training data.

Methods: We develop a novel string kernel MHC2SK (MHC-II String Kernel) method to measure the similarities among peptides with variable lengths.

Molecularly imprinted matrix solid-phase dispersion for extraction of chloramphenicol in fish tissues coupled with high-performance liquid chromatography determination.

The synthesis and evaluation of a molecularly imprinted polymer (MIP) as a selective matrix solid-phase dispersion (MSPD) sorbent, coupled with high-performance liquid chromatography for the efficient determination of chloramphenicol (CAP) in fish tissues are studied. The polymer was prepared using CAP as the template molecule, vinylpyridine as the functional monomer and ethylene glycol dimethacrylate as the cross-linking monomer, and sodium dodecyl sulfate as the surfactant in the presence of water as a solvent by miniemulsion polymerization. The CAP-imprinted polymers and nonimprinted polymers (NIPs) were characterized by Fourier transform IR spectroscopy, scanning electron microscopy, and static adsorption experiments.

Analysis of sulfamerazine in pond water and several fishes by high-performance liquid chromatography using molecularly imprinted solid-phase extraction.

The synthesis and evaluation of a molecularly imprinted polymer (MIP) used as a selective solid-phase extraction sorbent and coupled to high-performance liquid chromatography (HPLC) for the efficient determination of sulfamerazine (SMR) in pond water and three fishes are reported. The polymer was prepared using SMR as the template molecule, methacrylic acid as the functional monomer and ethylene glycol dimethacrylate as the crosslinking monomer in the presence of tetrahydrofuran as the solvent. The SMR-imprinted polymers and nonimprinted polymers were characterized by FT-IR and static adsorption experiments.

Analysis of free amino acids in islets of Langerhans by high-performance liquid chromatography using pre-column derivatization with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole.

A simple high-performance liquid chromatographic method with pre-column derivatization and fluorescence detection was developed and used for the analysis of free amino acids in islets of Langerhans; 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) served as pre-column derivatization reagent. Islets of Langerhans were separated from the pancreas of normal and obese rats, treated with pre-cooling methanol-water (80:20, v/v), and ultrasonicated to fragmentize the islets and effect deproteination. Several parameters influencing the derivatization reaction and chromatographic separation were optimized.

Determination of tetrandrine and fangchinoline in plasma samples using hollow fiber liquid-phase microextraction combined with high-performance liquid chromatography.

Tetrandrine (TET) and fangchinoline (FAN) are basic and highly hydrophobic drugs with logP>5.7. In this work, a simple, inexpensive and efficient liquid-phase microextraction (LPME) technology combined with high-performance liquid chromatography (HPLC) was developed for the simultaneous analysis of tetrandrine and fangchinoline in plasma samples.