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We have developed a web server that implements two complementary methods toquantify the depth of ligand binding site (LBS) in protein-ligand complexes:the "secant plane" (SP) and "tangent sphere" (TS) methods. The proteinmolecular centroid (global centroid, GC), and the LBS centroid (local centroid,LC) are first determined. The SP is the plane passing through the LC and normalto the line passing through the LC and the GC. The "exterior side" of the SP isthe side opposite GC. The TS is the sphere with center at GC and tangent to theSP at LC. The percentage of protein atoms inside the TS (TS index) and on theexterior side of the SP (SP index), are complementary measures of LBS depth.The SPi is directly proportional to LBS depth while the TSi is inverselyproportional. We tested the two methods using a test set of 67well-characterized protein-ligand structures (Laskowski, et al. 1996), as wellas that of an artificial protein in the form of a grid of points in the overallshape of a sphere and in which LBS of any depth can be specified. Results fromboth the SP and TS methods agree well with reported data (ibid.), and resultsfrom the artificial case confirm that both methods are suitable measures of LBSdepth. The web server may be used in two modes. In the "ligand mode", userinputs the protein PDB coordinates as well as those of the ligand. The "LBSmode" is the same as the former, except that the ligand coordinates are assumedto be unavailable; hence the user inputs what s/he believes to be thecoordinates of the LBS amino acid residues. In both cases, the web serveroutputs the SP and TS indices. LBS depth is usually directly related to theamount of conformational change a protein undergoes upon ligand binding -ability to quantify it could allows meaningful comparison of proteinflexibility and dynamics. The URL of our web server will be announced publiclyin due course.

Size-Independent Quantification of Ligand Binding Site Depth in Receptor Proteins