PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
| Autor: | Jens Erik Nielsen, J. Andrew McCammon, Todd J. Dolinsky, Nathan A. Baker |
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| Jazyk: | angličtina |
| Rok vydání: | 2004 |
| Předmět: |
Implicit solvation
Static Electricity Biomolecular structure Biology computer.software_genre Bioinformatics Force field (chemistry) Genetics Atomic charge Statistical physics Databases Protein Mathematical Computing Internet Molecular Structure Proteins Hydrogen Bonding computer.file_format Articles Poisson–Boltzmann equation Protein Data Bank Electrostatics Solvents Web service computer Software Hydrogen |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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