A fast, simplified potential-based approach is presented that estimates the protein− ligand
binding affinity based on the given 3D structure of a protein− ligand complex. This general …

Computational methods have become standard in today's medicinal chemistry tool kit. Like
any tool, it is important to periodically evaluate utility and ask how function can be improved …

Several different functions have been put forward for evaluating the energetics of ligand
binding to proteins. Those employed in the DOCK, GOLD and FlexX docking programs have …

We report here a computationally fast protocol for predicting binding affinities of non-metallo
protein–ligand complexes. The protocol builds in an all atom energy based empirical …

Abstract Knowledge-based scoring functions have recently emerged as an alternative and
very promising way of ranking protein-ligand complexes with known 3D structure according …

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 …

We present a novel atom–atom potential derived from a database of protein–ligand
complexes. First, we clarify the similarities and differences between two statistical potentials …

We have developed Bleep (biomolecular ligand energy evaluation protocol), an atomic level
potential of mean force (PMF) describing protein–ligand interactions. The pair potentials for …

We have developed an iterative knowledge-based scoring function (ITScore) to describe
protein–ligand interactions. Here, we assess ITScore through extensive tests on native …

The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …