QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock)

✍ Scribed by Brian B. Goldman; W. Todd Wipke

• Book ID: 101227568
• Publisher: John Wiley and Sons
• Year: 2000
• Tongue: English
• Weight: 364 KB
• Volume: 38
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(20000101)38:1<79::aid-prot9>3.0.co;2-u

✦ Synopsis

We present a new shape-based polynomial time algorithm for the rapid docking of rigid ligands into their macromolecular receptors. The method exploits molecular surface complementarity existing between a putative ligand and its receptor protein. Molecular shapes are represented by using a new shape descriptor that is based on local quadratic approximations to the molecular surface. The quadratic shape descriptor is capable of representing a plethora of molecular shapes and is not limited to describing convex or concave regions of molecular surface. A single pair of complementary descriptors is sufficient for computing the transformation matrix that positions a ligand into the receptor site. We demonstrate the capabilities of our algorithm by successfully reproducing the crystallographically determined orientation for a test set of 20 ligand-protein complexes. Proteins 2000;38