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propka graphical user interface (gui)  (Molecular Dynamics Inc)
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Molecular Dynamics Inc propka graphical user interface (gui)
The <t>PROPKA</t> <t>GUI</t> . (A) The main window of the PROPKA GUI for accessing general pK a information about the ionizable residues and their contributions to the pH-dependent free energy of unfolding. (B) The structure display window of VMD for an interactive access to the pK a data for particular ionizable residues. It depicts the structure of Bacillus circulans xylanase [PDB: 1XNB ] as it is displayed, by default, after the structure and the pK a data are loaded, using simplified-style drawing method.
Propka Graphical User Interface (Gui), supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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propka graphical user interface (gui) - by Bioz Stars, 2026-10
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The PROPKA GUI . (A) The main window of the PROPKA GUI for accessing general pK a information about the ionizable residues and their contributions to the pH-dependent free energy of unfolding. (B) The structure display window of VMD for an interactive access to the pK a data for particular ionizable residues. It depicts the structure of Bacillus circulans xylanase [PDB: 1XNB ] as it is displayed, by default, after the structure and the pK a data are loaded, using simplified-style drawing method.

Journal: BMC Structural Biology

Article Title: Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

doi: 10.1186/1472-6807-11-6

Figure Lengend Snippet: The PROPKA GUI . (A) The main window of the PROPKA GUI for accessing general pK a information about the ionizable residues and their contributions to the pH-dependent free energy of unfolding. (B) The structure display window of VMD for an interactive access to the pK a data for particular ionizable residues. It depicts the structure of Bacillus circulans xylanase [PDB: 1XNB ] as it is displayed, by default, after the structure and the pK a data are loaded, using simplified-style drawing method.

Article Snippet: The PROPKA Graphical User Interface (GUI) presented in this paper is developed to facilitate exploration of the pH-dependent protein properties in a convenient manner by providing a direct link between the structure and the pK a data, predicted by the PROPKA calculations, via the Visual Molecular Dynamics (VMD) program [ ].

Techniques:

Ionizable residues and pK a determinants in the xylanase structure . (A) The figure shows four ionizable residues with the most shifted pK a values in the structure of Bacillus circulans xylanase [PDB: 1XNB ] displayed using the PROPKA GUI. Labels next to each residue give: one-letter residue code with its residue ID, the pK a value and the shift of the pK a from its model value. (B) When an ionizable residue is selected (in this case tyrosine 80), all of its pK a determinants are displayed together with their contributions to the pK a shift shown with the appropriate labels.

Journal: BMC Structural Biology

Article Title: Graphical analysis of pH-dependent properties of proteins predicted using PROPKA

doi: 10.1186/1472-6807-11-6

Figure Lengend Snippet: Ionizable residues and pK a determinants in the xylanase structure . (A) The figure shows four ionizable residues with the most shifted pK a values in the structure of Bacillus circulans xylanase [PDB: 1XNB ] displayed using the PROPKA GUI. Labels next to each residue give: one-letter residue code with its residue ID, the pK a value and the shift of the pK a from its model value. (B) When an ionizable residue is selected (in this case tyrosine 80), all of its pK a determinants are displayed together with their contributions to the pK a shift shown with the appropriate labels.

Article Snippet: The PROPKA Graphical User Interface (GUI) presented in this paper is developed to facilitate exploration of the pH-dependent protein properties in a convenient manner by providing a direct link between the structure and the pK a data, predicted by the PROPKA calculations, via the Visual Molecular Dynamics (VMD) program [ ].

Techniques: Residue