The search for chemical hit material is a lengthy and increasingly expensive drug discovery process. To improve it, ligand-based quantitative structure-activity relationship models have been broadly applied to optimize primary and secondary compound ...
Machine-learning-based scoring functions (MLSFs) have gained attention for their potential to improve accuracy in binding affinity prediction and structure-based virtual screening (SBVS) compared to classical SFs. Developing accurate MLSFs for SBVS r...
BACKGROUND: Cell-cell communication in a tumor microenvironment is vital to tumorigenesis, tumor progression and therapy. Intercellular communication inference helps understand molecular mechanisms of tumor growth, progression and metastasis.
The core of large-scale drug virtual screening is to select the binders accurately and efficiently with high affinity from large libraries of small molecules in which non-binders are usually dominant. The binding affinity is significantly influenced ...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 5, 2023
The intermolecular interactions between proteins and ligands occur through site-specific amino acid residues in the proteins, and the identification of these key residues plays a critical role in both interpreting protein function and facilitating dr...
Generative neural networks trained on SMILES can design innovative bioactive molecules . These so-called chemical language models (CLMs) have typically been trained on tens of template molecules for fine-tuning. However, it is challenging to apply CL...
The application of artificial intelligence (AI) approaches to drug discovery for G protein-coupled receptors (GPCRs) is a rapidly expanding area. Artificial intelligence can be used at multiple stages during the drug discovery process, from aiding ou...
Journal of biomolecular structure & dynamics
May 22, 2023
Cancer accounts for the majority of deaths worldwide, and the increasing incidence of breast cancer is a matter of grave concern. Poly (ADP-ribose) polymerase-1 (PARP-1) has emerged as an attractive target for the treatment of breast cancer as it has...
Journal of chemical information and modeling
May 11, 2023
Over the past few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs th...
Proceedings of the National Academy of Sciences of the United States of America
Apr 24, 2023
With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics is encoded by the primary protein sequence so as to better predict ...