Journal of chemical information and modeling
Sep 29, 2021
The protein kinase family contains many promising drug targets. Many kinase inhibitors target the ATP-binding pocket, leading to approved drugs in past decades. Scaffold hopping is an effective approach for drug design. The kinase ATP-binding pocket ...
Journal of chemical theory and computation
Sep 23, 2021
Scoring functions are the essential component in molecular docking methods. An accurate scoring function is expected to distinguish the native ligand pose from decoy poses. Our previous experience (Pei et al. 2019, 59 (7), 3305-3315) proved that com...
The prediction of human leukocyte antigen (HLA) class II binding peptides plays important roles in understanding the mechanism of immune recognition and developing effective epitope-based vaccines. In this work, gated recurrent unit (GRU)-based recur...
Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide...
Prediction of T-cell receptor (TCR) interactions with MHC-peptide complexes remains highly challenging. This challenge is primarily due to three dominant factors: data accuracy, data scarceness, and problem complexity. Here, we showcase that "shallow...
The current pandemic outbreak clearly indicated the urgent need for tools allowing fast predictions of bioactivity of a large number of compounds, either available or at least synthesizable. In the computational chemistry toolbox, several such tools ...
IEEE journal of biomedical and health informatics
Sep 3, 2021
RNA-binding protein (RBP) is a powerful and wide-ranging regulator that plays an important role in cell development, differentiation, metabolism, health and disease. The prediction of RBPs provides valuable guidance for biologists. Although experimen...
Journal of chemical information and modeling
Sep 1, 2021
Machine learning scoring functions for protein-ligand binding affinity have been found to consistently outperform classical scoring functions when trained and tested on crystal structures of bound protein-ligand complexes. However, it is less clear h...
The activation of T cells is triggered by the interactions of T cell receptors (TCRs) with their epitopes, which are peptides presented by major histocompatibility complex (MHC) on the surfaces of antigen presenting cells (APC). While each TCR can on...
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucl...
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