PROPKA protocols

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PROPKA specifications

Information


Unique identifier OMICS_22471
Name PROPKA
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
Stability No
Maintained No

Maintainer


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

 (19)
2018
PMCID: 5908784
PMID: 29454620
DOI: 10.1016/j.bcp.2018.02.005

[…] and ctr:hct complexes were prepared for molecular dynamics simulations by means of a multistep procedure that integrates both python htmd and tcl (tool command language) scripts. the pdb2pqr and propka software were used to check the protein’s structural integrity and to add hydrogen atoms (configurations of titratable amino acid side chains were visually inspected) appropriate […]

2018
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7

[…] total score, and the top ranking five models were selected to initiate atomistic md simulations., the structures of protein molecules (actin, carp domain, wh2, and cap1248–474) were prepared using propka (pka estimation based on the crystallized complex and determination of protonation states at ph = 6.8), chimera (placing hydrogens), vmd (protein structure building and visualization), […]

2017
PMCID: 5307354
PMID: 28195200
DOI: 10.1038/srep42496

[…] parameters for water molecules and charmm-27 force-field parameters for the proteins and peptides were used. correct protonation state was assigned to all the protein and peptide residues using propka software. for tcr-unbound peptide-mhc complexes, we removed the tcr structure from the tri-molecular complex and performed md simulations of only the peptide-mhc complexes. for simulations […]

2017
PMCID: 5406204
PMID: 28445123
DOI: 10.7554/eLife.22175.024

[…] for p38α is applied throughout., each simulated system was generated using charmm27 force field (; ; ) at ph 7.4. the protonation states of the residues were determined both by h++ server () and propka3.0 () which gave identical results leaving all the residues in their usual charge states, except for his312 which was protonated. since the pka2 of phosphoric acid is measured at 6.7 and 7.2 […]

2017
PMCID: 5491310
PMID: 28617850
DOI: 10.1371/journal.pcbi.1005603

[…] 4zw9) using modeller 9v12[]. for xyle, we selected the inward-occluded structure (pdb id: 4ja3), and modeled all missing loops using the outward-occluded conformation (pdb id: 4gby) as the template. propka 3.1[,] was used to determine the protonation states of titratable residues other than asp27 in xyle at ph 7.0. in specific, glu206 was neutralized in both xyle systems. xyle was inserted […]


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PROPKA in publications

 (315)
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7

[…] total score, and the top ranking five models were selected to initiate atomistic md simulations., the structures of protein molecules (actin, carp domain, wh2, and cap1248–474) were prepared using propka (pka estimation based on the crystallized complex and determination of protonation states at ph = 6.8), chimera (placing hydrogens), vmd (protein structure building and visualization), […]

PMCID: 5935735
PMID: 29728603
DOI: 10.1038/s41598-018-25479-5

[…] electrostatic stabilization of the negative charge on the tyrosine leading to the unfavorable deprotonation free energy in the protein relative to solvent. this result is an agreement with the propka prediction for the pka of y202 of 15.0 pka units. overall, in contrast to the early hypothesis made based on the crystal structure, y202 strongly prefers to be in the protonated neutral form […]

PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] the transporter (supplementary table ). initially, the protein was oriented in the membrane using the online server orientation of proteins in membranes (opm). titratable states were addressed with propka calculation in the membrane framework with apbsmem, v2.0.2. next, the transporter was inserted in each of the 8 states described in supplementary table […]

PMCID: 5906587
PMID: 29706896
DOI: 10.3389/fphys.2018.00362

[…] 9.10) (webb and sali, ), using a cx26 crystal structure (maeda et al., ) as a template. the prediction of pka values of ionizable groups in cx36 was based on the 3d structure and was performed with propka (version 3.0) (olsson et al., ; søndergaard et al., )., electrophysiological measurements were performed using hela (human cervix carcinoma cells, atcc ccl2) cells transfected with wild type […]

PMCID: 5924399
PMID: 29642450
DOI: 10.3390/brainsci8040063

[…] modeller 9v17 [] homology models of the terminal domains for rdat. based on the align module of modeller 9v17 [], two functional na+ and one cl− ion in 4xp1 were also added to the s1 binding site. propka [] was used to determine the protonated state of the ionizable glu490 residue of rdat while a disulfide bond was introduced in el2, between cys180 and cys189., compound preparation […]


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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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