fpocket: online tools for protein ensemble pocket detection and tracking

Abstract

Computational small-molecule binding site detection has several important applications in the biomedical field. Notable interests are the identification of cavities for structure-based drug discovery or functional annotation of structures. fpocket is a small-molecule pocket detection program, relying on the geometric alpha-sphere theory. The fpocket web server allows: (i) candidate pocket detection--fpocket; (ii) pocket tracking during molecular dynamics, in order to provide insights into pocket dynamics--mdpocket; and (iii) a transposition of mdpocket to the combined analysis of homologous structures--hpocket. These complementary online tools allow to tackle various questions related to the identification and annotation of functional and allosteric sites, transient pockets and pocket preservation within evolution of structural families. The server and documentation are freely available at http://bioserv.rpbs.univ-paris-diderot.fr/fpocket.

Figure 1.

Workflow of the pocket tracking methodology. α-spheres from different snapshots are represented by different colors (dark and light).

Figure 2.

(A) fpocket server provides a set of target structure pictures, showing predicted pockets as surfaces of each pockets atoms (one color per pocket). (B) The fpocket results page embeds both Jmol and OpenAstexViewer (used here) applets for a quick analysis of the predicted pockets. A control panel on the right part allows the selection of the pockets to visualize and switch between various molecular representations. Here, the surface of the residues of the pocket is in red, the α-spheres in magenta and green and the envelope of the pocket is represented using a green mesh.

Figure 3.

The mdpocket server provides a set of target structure pictures, showing superimposed PDB snapshots as ribbon (A) and the first snapshot structure molecular surface colored by α-spheres density ranging from blue (low density) to red (high density) (B). The mdpocket results page embeds the Jmol applet (C) to give an overview of the conserved cavities (the density grid is represented as an isosurface), and the right part provides viewing components and to extract cavity conservation at a user-selected isovalue—for more details see the main text. It is possible (D) to map the density information onto the residues to explore pocket stability in the structure. Here, residues corresponding to high-density regions are displayed as molecular surfaces in the OpenAstexViewer.

Figure 4.

(A) Result of a run in Mode 1 of mdpocket on 17 snapshots of a MD trajectory of Ahb1 FB10L. A pocket density grid is provided, allowing visualization of conserved pockets and open channels during the MD trajectory. Analysis shows that the exit pathway of CO is closed in this mutant and that a secondary cavity beneath the heme group is existing. (B) Illustration of the results obtained in (35).

Figure 5.

Tracking the volume of the channel between the upper heme pocket and lower heme pocket (mdpocket Mode 2). The pocket grid is shown as red spheres. (A) Y145 in the closed state is situated in the pocket, (B) Y145 in the open state is situated on the edge pocket. (C) smoothed volume of the pocket (black curve) versus time, the distance between the hydroxyl group of Y145 and the heme versus time is represented in red.

Figure 6.

Volume of the P38-binding site during a 50 ns trajectory. Gray line, volume estimated for each snapshot; light gray line: smoothed volume.