pdb2pqr
Preparation of protein structures for electrostatics calculations
Install
- All systems
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curl cmd.cat/pdb2pqr.sh
- Debian
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apt-get install pdb2pqr - Ubuntu
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apt-get install pdb2pqr - Kali Linux
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apt-get install pdb2pqr - Windows (WSL2)
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sudo apt-get updatesudo apt-get install pdb2pqr - Raspbian
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apt-get install pdb2pqr - Dockerfile
- dockerfile.run/pdb2pqr
pdb2pqr
Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides 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 This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues.