3V: cavity, channel and cleft volume calculator and extractor - PubMed (original) (raw)

. 2010 Jul;38(Web Server issue):W555-62.

doi: 10.1093/nar/gkq395. Epub 2010 May 16.

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3V: cavity, channel and cleft volume calculator and extractor

Neil R Voss et al. Nucleic Acids Res. 2010 Jul.

Abstract

As larger macromolecular structures become available, there is a growing need to understand their 'internal' volumes--such as deep clefts, channels and cavities--as these often play critical roles in their function. The 3V web server can automatically extract and comprehensively analyze all the internal volumes from input RNA and protein structures. It rapidly finds internal volumes by taking the difference between two rolling-probe solvent-excluded surfaces, one with as large as possible a probe radius and the other with a solvent radius (typically 1.5 A for water). The outputs are volumetric representations, both as images and downloadable files, which can be used for further analysis. The 3V server and source code are available from http://3vee.molmovdb.org.

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Figures

Figure 1.

Figure 1.

Richards’ rolling probe definition. Two sphere of radius _R_1 and _R_2 are shown rolling across the surface of a macromolecule defined by the 12 atoms. The excluded surface is the surface defined by the exterior of the each sphere (dashed line) as they roll across the array of atoms By subtracting the enclosed volume of the smaller sphere (_R_1) from the enclosed volume of the larger sphere (_R_2) the solvent volume (blue) is obtained. Figure adapted from Richards, 1977 (26).

Figure 2.

Figure 2.

Effects of the rolling probe method. (A) The rolling probe volumes at different probe radii. From left to right, the excluded surface at probe radius 10.0, 6.0, 3.0, 1.5 (water-excluded surface) and 0.0 Å (van der Waals surface). (B) Shell volume (probe radius of 6.0 Å), solvent-excluded volume (probe radius of 1.5 Å), and solvent volume (blue). The solvent volume is determined by subtracting the solvent-excluded volume from the shell volume. In both (A) and (B), the top model is the hammerhead ribozyme structure (29) and the bottom is the lysozyme structure (30).

Figure 3.

Figure 3.

Slices through the macromolecule volumes showing the channels and cavities. The two macromolecules shown are (A) lysozyme (30) and (B) the 50S ribosomal subunit (33). Four volumes are shown: the van der Waals volume in green, the solvent-excluded surface in yellow, channel volume in blue, and the cavity volume in pink. The shell volume is equal to all the colored areas combined.

Figure 4.

Figure 4.

Results from the five general use tools. Results of running each of the five available general use tools on the p-glycoprotein structure (34). The Volume Calculation tool creates a single excluded surface of any molecule at any probe radius, shown is the van der Waals radius of 0.0 Å. The Volume Range Calculation tool calculates the excluded surface at several different probe radii, shown are probe radii of 0.0, 3.0, 6.0 and 9.0 Å with volumes ranging from 117 970 to 232 799 Å3. The Solvent Extract finds all the solvent in a structure, independent of the size of the volume. In this case, the solvent occupied a volume of 13 487 Å3. The Channel Extract tool produced the chosen cleft from the structure. The Channel Find tool found a single, large channel in the structure with a volume of 10 764 Å3. At the bottom, right the channel found by the Channel Find tool is shown within a ribbons model of the PDB structure.

Figure 5.

Figure 5.

Web page structure. (A) The flow of the web page. The first web page presented is the tool selection page with links to run each of the six tools. A typical tool interface page, including the parameter input table and preset buttons. While the calculations are being performed, a progress page is presented with program output. After the program finishes, the progress page becomes the results page. The results page contains information about each calculated volume. (B–E) A detail of the results page provides the details of each calculated volume. Each results page contains four major components: (B) run information, such as the PDB ID and other input parameters, (C) image snapshots of the volume, (D) volume information, including the total volume, surface area, sphericity, and other statistics, and (E) links to download and display the volume.

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