PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Washington University in St. Louis · University of Copenhagen · +2 more institutions
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…
Citation impact
- FWCI
- 10.36
- Percentile
- 100%
- References
- 33
Authors
7- TJT. J. DolinskyCorresponding
Washington University in St. Louis, University of Copenhagen, University of Nebraska–Lincoln, University College Dublin
- PCPaul Czodrowski
University of Nebraska–Lincoln, University College Dublin, University of Copenhagen, Washington University in St. Louis
- HLHui Li
Washington University in St. Louis, University of Copenhagen, University College Dublin, University of Nebraska–Lincoln
- JEJens Erik Nielsen
University College Dublin, Washington University in St. Louis, University of Nebraska–Lincoln, University of Copenhagen
- JHJan H. Jensen
University of Copenhagen, Washington University in St. Louis, University of Nebraska–Lincoln, University College Dublin
Topics & keywords
- Computer science
- Software
- Computational science
- File format
- Protein Data Bank (RCSB PDB)
- XML
- Biomolecule
- Source code