Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents too...
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identif...
Journal of chemical information and modeling
Aug 19, 2020
Deep learning has demonstrated significant potential in advancing state of the art in many problem domains, especially those benefiting from automated feature extraction. Yet, the methodology has seen limited adoption in the field of ligand-based vir...
In combinatorial chemical approaches, optimizing the composition and arrangement of building blocks toward a particular function has been done using a number of methods, including high throughput molecular screening, molecular evolution, and computat...
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding ce...
Journal of chemical information and modeling
Aug 4, 2020
Current deep learning methods for structure-based virtual screening take the structures of both the protein and the ligand as input but make little or no use of the protein structure when predicting ligand binding. Here, we show how a relatively simp...
In the last decade, machine learning and artificial intelligence applications have received a significant boost in performance and attention in both academic research and industry. The success behind most of the recent state-of-the-art methods can be...
Information embedded in ligand-binding residues (LBRs) of proteins is important for understanding protein functions. How to accurately identify the potential ligand-binding residues is still a challenging problem, especially only protein sequence is ...
DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value. We demonstrate a new approach applying machine learning to DEL selection data by identifying active molecul...
Journal of chemical theory and computation
Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
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