ENHANCED PDB2PQR WITH ADVANCED PKA CALCULATIONS

$3,181P41FY2009RRNIH

University Of California, San Diego, La Jolla CA

Investigators

Linked publications & trials

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: Adding a limited number of missing heavy atoms to biomolecular structures Determining side-chain pKas Placing missing hydrogens Optimizing the protein for favorable hydrogen bonding Assigning charge and radius parameters from a variety of force fields

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