Machine learning (ML) systems can model quantitative structure-property relationships (QSPR) using existing experimental data and make property predictions for new molecules. With the advent of modalities such as targeted protein degraders (TPD), the...
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many dise...
Journal of chemical information and modeling
Jul 2, 2024
Message passing neural networks (MPNNs) on molecular graphs generate continuous and differentiable encodings of small molecules with state-of-the-art performance on protein-ligand complex scoring tasks. Here, we describe the proximity graph network (...
IEEE journal of biomedical and health informatics
Jul 2, 2024
Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches usually transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then ...
International journal of molecular sciences
Jun 30, 2024
Chimeric antigen receptor (CAR) T cells represent a revolutionary immunotherapy that allows specific tumor recognition by a unique single-chain fragment variable (scFv) derived from monoclonal antibodies (mAbs). scFv selection is consequently a funda...
Journal of chemical information and modeling
Jun 26, 2024
The intricate interaction between major histocompatibility complexes (MHCs) and antigen peptides with diverse amino acid sequences plays a pivotal role in immune responses and T cell activity. In recent years, deep learning (DL)-based models have eme...
As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems a...
Intracellular tau fibrils are sources of neurotoxicity and oxidative stress in Alzheimer's. Current drug discovery efforts have focused on molecules with tau fibril disaggregation and antioxidation functions. However, recent studies suggest that memb...
International journal of molecular sciences
Jun 13, 2024
Human infection with the coronavirus disease 2019 (COVID-19) is mediated by the binding of the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the human angiotensin-converting enzyme 2 (ACE2). The frequent mutatio...
BACKGROUND: Protein-peptide interaction prediction is an important topic for several applications including various biological processes, understanding drug discovery, protein function abnormal cellular behaviors, and treating diseases. Over the year...
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