QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).
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.
Goldman
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BB
Department of Chemistry, University of California, Santa Cruz 95064, USA.
Wipke
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WT
D000465:Algorithms; D003198:Computer Simulation; D005492:Folic Acid / Q000737:chemistry; D008024:Ligands; D046911:Macromolecular Substances; D008727:Methotrexate / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry; D014867:Water / Q000737:chemistry
D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins; D014867:Water; D005492:Folic Acid; D013762:Tetrahydrofolate Dehydrogenase; D008727:Methotrexate