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Protocols

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). https://github.com/jensengroup/propka-3.1

Publications for PROPKA

PROPKA citations

 (395)
call_split

Structural basis of actin monomer re charging by cyclase associated protein

2018
Nat Commun
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7
call_split See protocol

[…] heir 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), and PyTo […]

library_books

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue

2018
Sci Rep
PMCID: 5935735
PMID: 29728603
DOI: 10.1038/s41598-018-25479-5

[…] rovide 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 in […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
Nat Commun
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] f 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  into a 1-palmitolyl-2-oleoyl-sn-glycero- […]

call_split

Modulation of Connexin 36 Gap Junction Channels by Intracellular pH and Magnesium Ions

2018
Front Physiol
PMCID: 5906587
PMID: 29706896
DOI: 10.3389/fphys.2018.00362
call_split See protocol

[…] n 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., ). […]

library_books

Mechanistic Insights into the Stimulant Properties of Novel Psychoactive Substances (NPS) and Their Discrimination by the Dopamine Transporter—In Silico and In Vitro Exploration of Dissociative Diarylethylamines

2018
Brain Sci
PMCID: 5924399
PMID: 29642450
DOI: 10.3390/brainsci8040063

[…] de 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 and docking. T […]

call_split

Extracellular loops 2 and 3 of the calcitonin receptor selectively modify agonist binding and efficacy

2018
PMCID: 5908784
PMID: 29454620
DOI: 10.1016/j.bcp.2018.02.005
call_split See protocol

[…] CT 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 for a simulat […]

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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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