title: PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
abstract: Real-world observable physical and chemical characteristics are increasingly being calculated from the 3D structures of biomolecules. Methods for calculating pK(a) 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 pK(a) 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.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Center for Computational Biology, Washington University in St. Louis, 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110, USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Dolinsky
authors.forename: Paul
authors.initials: P
authors.lastname: Czodrowski
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Jens E
authors.initials: JE
authors.lastname: Nielsen
authors.forename: Jan H
authors.initials: JH
authors.lastname: Jensen
authors.forename: Gerhard
authors.initials: G
authors.lastname: Klebe
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Baker
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D020407:Internet; D008024:Ligands; D008432:Mathematical Computing; D008968:Molecular Conformation; D015394:Molecular Structure; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D012984:Software; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
chemical_list: D008024:Ligands; D011506:Proteins; D012997:Solvents; D006859:Hydrogen