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

B B Goldman; W T Wipke

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PubMed · 10651041

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

B B Goldman·W T Wipke

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Abstract

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.

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Algorithms Computer Simulation Folic Acid Ligands Macromolecular Substances Methotrexate Models, Molecular Protein Conformation Proteins Tetrahydrofolate Dehydrogenase Water Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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B B Goldman, W T Wipke. 2000-01-01. QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock).. https://pubmed.ncbi.nlm.nih.gov/10651041/

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