PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

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ID: 291107
2007
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Abstract
Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pKa values, binding constants of ligands, and changes in protein stability are readily available, but often the limiting step in computational biology is the conversion of PDB structures into formats ready for use with biomolecular simulation software. The continued sophistication and integration of biomolecular simulation methods for systems- and genome-wide studies requires a fast, robust, physically realistic and standardized protocol for preparing macromolecular structures for biophysical algorithms. As described previously, the PDB2PQR web server addresses this need for electrostatic field calculations (Dolinsky et al., Nucleic Acids Research, 32, W665–W667, 2004). Here we report the significantly expanded PDB2PQR that includes the following features: robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code. These features are available through a new web interface (http://pdb2pqr.sourceforge.net/), which offers users a wide range of options for PDB file conversion, modification and parameterization.
Reference Key
openalex_W2165565773 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors T. J. Dolinsky, Paul Czodrowski, Hui Li, Jens Erik Nielsen, Jan H. Jensen, G. Klebe, Nathan Baker
Journal Nucleic Acids Research
Year 2007
DOI
10.1093/nar/gkm276
URL
https://academic.oup.com/nar/article-pdf/35/suppl_2/W522/9584314/gkm276.pdf
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