Journal of chemical information and modeling
Sep 9, 2022
Water molecules at the ligand-protein interfaces play crucial roles in the binding of the ligands, but the behavior of protein-bound water is largely ignored in many currently used machine learning (ML)-based scoring functions (SFs). In an attempt to...
BACKGROUND: Accurately predicting drug-target binding affinity (DTA) in silico plays an important role in drug discovery. Most of the computational methods developed for predicting DTA use machine learning models, especially deep neural networks, and...
Journal of chemical information and modeling
Sep 6, 2022
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The typical methods for computing the...
Three-dimensional protein structure prediction is one of the major challenges in bioinformatics. According to recent research findings, real-valued distance prediction plays a vital role in determining the unique three-dimensional protein structure. ...
To understand the origin of disease comorbidity and to identify the essential proteins and pathways underlying comorbid diseases, we developed LeMeDISCO (Large-Scale Molecular Interpretation of Disease Comorbidity), an algorithm that predicts disease...
Proteins are constructed from amino acid sequences. Their structural classifications include primary, secondary, tertiary, and quaternary, with tertiary and quaternary structures influencing protein function. Because a protein's structure is inextric...
Hydration free energy (HFE) is a key factor in improving protein-ligand binding free energy (BFE) prediction accuracy. The HFE itself can be calculated using the three-dimensional reference interaction model (3D-RISM); however, the BFE predictions so...
Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS)...
Computational identification of human-virus protein-protein interactions (PHIs) is a worthwhile step towards understanding infection mechanisms. Analysis of the PHI networks is important for the determination of pathogenic diseases. Prediction of the...
Journal of computational biology : a journal of computational molecular cell biology
Aug 10, 2022
The scientific community is rapidly generating protein sequence information, but only a fraction of these proteins can be experimentally characterized. While promising deep learning approaches for protein prediction tasks have emerged, they have comp...