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

By A. W. Schüttelkopf, D. V. van Aalten. 2004

4,547 citations recorded by the source corpus.

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.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

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Citations in the corpus

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands (2017, methodology): “Lastly, the PRODRG (27) server provides GROMOS FF parameters and charges in a GROMACS formatted file.”
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes (2024, neutral): “…residue is automatically determined with the software reduce 41 , all-atom structures are converted to coarse-grained representations if this option was selected and parameters and topologies are automatically generated for small molecules by using an in-house version of the software PRODRG 42 .”
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets (2007, methodology): “25 As in our previous CAPRI submissions, HADDOCK was driven by data derived from literature and/or interface predictions.”
CB-Dock: a web server for cavity detection-guided protein–ligand blind docking (2019, methodology): “The Nutlin-3a mol2 ﬁ le was generated by the PRODRG software [49].”
The HADDOCK web server for data-driven biomolecular docking (2010, background): “Enable the use of symmetry.”
The targets of CAPRI rounds 20–27 (2013, methodology): “It was built by A. Basle with the ligand modeling software PRODRG,9 and had the sugar rings in an arbitrary conformation.”