Dr. Czirják Gábor

Semmelweis Egyetem, Élettani Intézet

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PrinCCes

 Protein internal Channel & Cavity estimation

Aquaporin 1 central channel.

The transmembrane central channel of aquaporin 1 was determined automatically by PrinCCes as void 1, which is located between the subunits of the tetrameric protein complex. The extracellular (upper) and intracellular (lower) entrances are illustrated in lime color. On the intracellular side eight openings were detected by PrinCCes. The (finely) triangulated void surface and the ribbon representation of the protein chains were visualized as rotatable 3D objects in VMD software with the graphic user interface (GUI) version of PrinCCes.

PrinCCes is a free* computer program for the automatic visualization of voids in proteins or protein complexes. The input of the program is the PDB (Protein Data Bank) file of the structure. A major design principle was user friendly operation. Practically, no bioinformatics knowledge is required for the graphic user interface (GUI) versions. The software detects all voids (pockets, crevices, chambers, tunnels, etc.). The resolution of the analysis and the size range for the void search are controlled by three easy-to-understand parameters (grid resolution, radius of small probe sphere – which freely moves within the voids, and radius of large probe sphere – which cannot enter the voids). The voids of a protein can be visualized one by one or in any user-specified combinations as triangulated surfaces in response to a click. The output is automatically exported to free VMD (Visual Molecular Dynamics) or UCSF Chimera software, allowing the 3D rotation of the surfaces and the production of publication quality images.

PrinCCes is available as GUI and CMD (command line) versions for Windows and Linux on 32 and 64 bit platforms.

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Czirjak, G.: PrinCCes: continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins. J Mol Graph Model 62: 118-127, 2015

Humphrey W, Dalke A, and Schulten K. VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 1996.

Sui H, Han BG, Lee JK, Walian P, and Jap BK. Structural basis of water-specific transport through the AQP1 water channel. Nature 414: 872-878, 2001.

Link to PrinCCes Audioslides Video tutorial

* You have to accept the licence agreement. The major requirement is that you agree to cite the above PrinCCes and VMD papers in your publications, if this software was used.

 

 

 

 

 

 

 

 

 

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