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Figure 2 | BMC Structural Biology

Figure 2

From: A simple method for finding a protein’s ligand-binding pockets

Figure 2

A given triangle on the convex hull for the PDB:1ABT structure. The three vertices are labeled as 1, 2, and 3. The point p is determined by the extreme values of x, y, and z of these three vertices. The distance of atom i to the triangle is obtained as follows: first obtain the normal vector to the triangle, N, N =(x 2 x 1 )×(x 3 x 1 ), where x1, x2, and x3 are the vectors from the origin of the systems of Cartesian coordinates to the three vertices. Then, calculate the angle between the normal vector and the line passing through atom i and one of the vertices of this triangle using the following relation: cosθ= x 1 x i · N x 1 x i N , Finally, we compute this distance by d i  = |x 1 x i | cos θ, where x i is a vector joining the origin and a given point in this volume.

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