Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …

Molecular docking is a computational method for predicting the placement of ligands in the
binding sites of their receptor (s). In this review, we discuss the methodological …

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely
available computer programs for the analysis and processing of time series of three …

This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …

A key metric to assess molecular docking remains ligand enrichment against challenging
decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for …

Recently much effort has been invested in using convolutional neural network (CNN)
models trained on 3D structural images of protein-ligand complexes to distinguish binding …

The estimation of free energy of binding is a key problem in structure-based design. We
developed the scoring function HYDE based on a consistent description of HYdrogen bond …

Molecular Docking is used to positioning the computer-generated 3D structure of small
ligands into a receptor structure in a variety of orientations, conformations and positions …

Chemical probes that form a covalent bond with a protein target often show enhanced
selectivity, potency, and utility for biological studies. Despite these advantages, protein …

Protein-ligand docking is currently an important tool in drug discovery efforts and an active
area of research that has been the subject of important developments over the last decade …