PROPKA pipeline

PROPKA specifications


Unique identifier OMICS_22471
Interface Web user interface
Restrictions to use None
Input data A PDB ID or a PDB file or a PDB web URL
Input format PDB
Computer skills Basic
Version 1.00
Maintained No


This tool is not available anymore.

Additional information

Supported by a grant from the National Science Foundation (MCB 209941).

Publications for PROPKA

PROPKA IN pipelines

PMCID: 4515779
PMID: 26205423
DOI: 10.1038/ncomms8622

[…] x-ray structure (pdbid 2zxe) and popc membrane was assembled with the charmm-gui membrane builder module495051 with 0.15 m kcl and 0.15 m nacl in the solution. on the basis of pka calculations with propka web server52535455 and the previous selectivity studies56, residues e334, e786, d815, d933, e960 and e961 were protonated. the complete system was equilibrated for 675 ps while reducing […]

PMCID: 4598623
PMID: 26417850
DOI: 10.1038/ncomms9393

[…] conditions to our previous simulations (see refs 16, 17 for details). the protonation states of all titratable residues in the crystal structure were assigned based on pka calculations using propka47 and the protonation sites were determined using molprobity36. the simulations were performed with namd 2.8–10 (ref. 48). a brief description of the protocols used in simulations listed […]

PMCID: 4242812
PMID: 25422503
DOI: 10.1085/jgp.201411219

[…] step; similarly, ion–carboxyl group distances were also calculated as the minimum distance to the two oxygen atoms. after the simulations, the pka values of titratable residues were estimated with propka 3.1 (søndergaard et al., 2011) using snapshots of the md simulations that were sampled every 1 ns. na+ ions within 6 å of the protein were taken into account because preliminary calculations […]

PROPKA institution(s)
Department of Chemistry, University of Iowa, Iowa City, IA, USA; Department of Physics and Astronomy, University of Iowa, Iowa City, IA, USA

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