Generative chemical language models (CLMs) can be used for de novo molecular structure
generation by learning from a textual representation of molecules. Here, we show that hybrid …

A novel and robust automated docking method that predicts the bound conformations of
flexible ligands to macromolecular targets has been developed and tested, in combination …

Motivation: Accurately predicting the binding affinities of large sets of diverse protein–ligand
complexes is an extremely challenging task. The scoring functions that attempt such …

Our comparative assessment of scoring functions (CASF) benchmark is created to provide
an objective evaluation of current scoring functions. The key idea of CASF is to compare the …

Molecular docking is a widely-used computational tool for the study of molecular recognition,
which aims to predict the binding mode and binding affinity of a complex formed by two or …

This paper describes the development of a simple empirical scoringfunction designed to
estimate the free energy of binding for aprotein–ligand complex when the 3D structure of the …

Surflex is a fully automatic flexible molecular docking algorithm that combines the scoring
function from the Hammerhead docking system with a search engine that relies on a surface …

The scoring function is one of the most important components in structure-based drug
design. Despite considerable success, accurate and rapid prediction of protein–ligand …

In this paper we describe the search strategies developed for docking flexible molecules to
macomolecular sites that are incorporated into the widely distributed DOCK software …

Recent advances in combinatorial chemistry and high-throughput screening have made it
possible for chemists to synthesize large numbers of compounds. However, this is still a …