PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
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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 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.
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The record
- Venue
- Nucleic Acids Research
- Topic
- Protein Structure and Dynamics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- National Center for Research ResourcesNational Institute of General Medical SciencesCentre National de la Recherche ScientifiqueCanada Excellence Research Chairs, Government of CanadaDeutsche ForschungsgemeinschaftNational Institutes of HealthScience Foundation IrelandNational Science Foundation
- Keywords
- Computer scienceSoftwareComputational scienceFile formatProtein Data Bank (RCSB PDB)XMLBiomoleculeSource codeForce field (fiction)Interface (matter)Biological systemBioinformaticsData miningBiologyNanotechnologyMaterials scienceDatabaseProgramming languageOperating systemArtificial intelligence
- Has abstract in OpenAlex
- yes