PRODRG: a tool for high-throughput crystallography of protein–ligand complexes

Abstract

The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG-generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors.

Cite this paper

Related papers

1. A short history of SHELX2007
2. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading2009
3. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility2009
4. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules2017
5. Overview of the CCP 4 suite and current developments2011