PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

By Todd J. Dolinsky, Jens Erik Nielsen, James Andrew McCammon, Nathan A. Baker. 2004

3,375 citations recorded by the source corpus.

Continuum solvation models, such as Poisson-Boltzmann and Generalized Born methods, have become increasingly popular tools for investigating the influence of electrostatics on biomolecular structure, energetics and dynamics. However, the use of such methods requires accurate and complete structural data as well as force field parameters such as atomic charges and radii. Unfortunately, the limiting step in continuum electrostatics calculations is often the addition of missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment of parameters to biomolecular structures. To address this problem, we have developed the PDB2PQR web service (http://agave.wustl.edu/pdb2pqr/). This server automates many of the common tasks of preparing structures for continuum electrostatics calculations, including adding a limited number of missing heavy atoms to biomolecular structures, estimating titration states and protonating biomolecules in a manner consistent with favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields, and finally generating 'PQR' output compatible with several popular computational biology packages. This service is intended to facilitate the setup and execution of electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 (2020, methodology): “AMDock integrates functionalities from Autodock Vina and Autodock4, ADT scripts, AutoLigand [15], Open Babel [16], PDB2PQR [17] and PyMOL [18].”
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm (2010, methodology): “Hydrogens were then added, and partial charges and radii were assigned to atoms using the program PDB2PQR [84].”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “The non-standard amino acid residues, heteroatoms (HETATM records), original hydrogen atoms and residues with incomplete backbone atoms are removed and the missing side chains are added by PDB2PQR (42).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “PDB2PQR (Dolinsky et al., 2004) was used to generate the PQR files for the electrostatics figures.”
Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. (2018, methodology): “Individual chains were extracted from Protein Data Bank (PDB) asymmetric units, and missing heavy atoms were restored by the PDB2PQR software (59) using CHARMM topology parameters (1).”