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Understanding the challenges of protein flexibility in drug design
(Taylor & Francis, 2015)
Introduction: Protein–ligand interactions play key roles in various metabolic pathways, and the proteins involved in these interactions represent major targets for drug discovery. Molecular docking is widely used to predict the structure of protein–ligand complexes, and protein flexibility stands out as one of the most important and challenging issues ...
DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach
Molecular docking is a standard computational approach to predict binding modes of protein–ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays ...
APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations
The Class I Major Histocompatibility Complex (MHC) is a central protein in immunology as it binds to intracellular peptides and displays them at the cell surface for recognition by T-cells. The structural analysis of bound peptide-MHC complexes (pMHCs) holds the promise of interpretable and general binding prediction (i.e., testing whether a given ...