Journal of chemical information and modeling
Jul 12, 2021
p is an important property in the lead optimization process since the charge state of a molecule in physiologic pH plays a critical role in its biological activity, solubility, membrane permeability, metabolism, and toxicity. Accurate and fast estima...
MicroRNAs (miRNAs) can serve as activation signals for membrane receptors, a recently discovered function that is independent of the miRNAs' conventional role in post-transcriptional gene regulation. Here, we introduce a machine learning approach, Br...
Abelson kinase (c-Abl) is a non-receptor tyrosine kinase involved in several biological processes essential for cell differentiation, migration, proliferation, and survival. This enzyme's activation might be an alternative strategy for treating disea...
Protein patterning has emerged as a powerful means to interrogate adhering cells. However, the tools to apply a sub-micrometer periodic stimulus and the analysis of the response are still being standardized. We propose a technique combining electron ...
Nowadays, more and more attention has been attracted to develop selective PI3Kγ inhibitors, but the unique structural features of PI3Kγ protein make it a very big challenge. In the present study, a virtual screening strategy based on machine learning...
This study unites six popular machine learning approaches to enhance the prediction of a molecular binding affinity between receptors (large protein molecules) and ligands (small organic molecules). Here we examine a scheme where affinity of ligands ...
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational...
: Structure-based virtual screening (SBVS) is an essential strategy for hit identification. SBVS primarily uses molecular docking, which exploits the protein-ligand binding mode and associated affinity score for compound ranking. Previous studies hav...
Accurate prediction of protein-ligand interactions can greatly promote drug development. Recently, a number of deep-learning-based methods have been proposed to predict protein-ligand binding affinities. However, these methods independently extract t...
International journal of molecular sciences
May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...