Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Jul 25, 2024
The binding of proteins and ligands is a crucial aspect of life processes. The calculation of the protein-ligand binding affinity (PLBA) offers valuable insights into protein function, drug screening targets protein receptors, and enzyme modification...
Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods-DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web...
MOTIVATION: Predicting protein-ligand binding affinity is crucial in new drug discovery and development. However, most existing models rely on acquiring 3D structures of elusive proteins. Combining amino acid sequences with ligand sequences and bette...
MOTIVATION: Deep graph learning (DGL) has been widely employed in the realm of ligand-based virtual screening. Within this field, a key hurdle is the existence of activity cliffs (ACs), where minor chemical alterations can lead to significant changes...
Accurate prediction of protein-ligand binding affinity (PLA) is important for drug discovery. Recent advances in applying graph neural networks have shown great potential for PLA prediction. However, existing methods usually neglect the geometric inf...
Small molecule drugs can be used to target nucleic acids (NA) to regulate biological processes. Computational modeling methods, such as molecular docking or scoring functions, are commonly employed to facilitate drug design. However, the accuracy of ...
Protein-ligand interaction prediction presents a significant challenge in drug design. Numerous machine learning and deep learning (DL) models have been developed to accurately identify docking poses of ligands and active compounds against specific t...
Accurately predicting the binding affinity between proteins and ligands is crucial in drug screening and optimization, but it is still a challenge in computer-aided drug design. The recent success of AlphaFold2 in predicting protein structures has br...
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct from the orthosteric site, is one of the most direct and efficient ways to fine-tune macromolecular function. The Allosteric Database (ASD; accessible onli...
Understanding the interactions between a ligand and its molecular target is crucial in guiding the optimization of molecules for any drug design workflow. Multiple experimental and computational methods have been developed to better understand these...