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W T Wipke

Publications and source records attributed to W T Wipke.

7 recordsLinked to original sources
PubMed2000

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.

Algorithms↗
PubMed1984

Artificial intelligence in organic synthesis. SST: starting material selection strategies. An application of superstructure search.

A program for the interactive selection of potential starting materials given a desired target molecule is described. The program uses hierarchical search to rapidly select candidates from a large starting material library and contains a function to evaluate the appropriateness of the functionality of the starting material. The user can specify restrictions on features such as the number of atoms in the starting material, price limitations, chirality, and whether to use superstructure or substructure searching. Several examples of the results of the program are presented.

Chemistry, Organic↗
PubMed1984

Rapid subgraph search using parallelism.

A new parallel processing algorithm is reported for subgraph matching. Parallelism is achieved for the first time within the process of node-by-node matching of two individual graphs. A SIMULA program is described for simulating this parallel subgraph search algorithm. Simulation results from a series of chemical substructure search problems show an average utilization of 84% on a 25-processor machine and up to a 24-fold speed enhancement over a single processor. Potential applications include starting material selections for synthesis as well as general substructure search problems.

Chemical Phenomena↗
PubMedDate not supplied

Quadratic shape descriptors. 1. Rapid superposition of dissimilar molecules using geometrically invariant surface descriptors.

In this paper, we present a novel approach to shape-based molecular similarity searching. The method that we introduce is able to superimpose dissimilar molecules by using geometrically invariant molecular surface descriptors. The shape descriptors are calculated by least-squares fitting of a quadratic function to small sections of the molecular surface of a ligand. Invariant geometric properties of the approximated surface patch are then extracted from the fitted quadratic function. The extracted properties are used to quantify the shape and to obtain a canonical orientation for this section of surface. The superimposition algorithm uses these geometric invariants to recognize similar regions of surface shape existing on two molecules and to bring these regions (and consequently the molecules) into registration. Because these geometric descriptors are based upon local surface shape, the superimposing algorithm is insensitive to the connectivity and the relative sizes of the molecules being matched. The capabilities of our algorithm are demonstrated by superimposing dissimilar ligands known to inhibit the same enzyme system. In all cases examined the algorithm generates superpositions that are in agreement with crystallographic results. The algorithm is also applied to align the two different proteins on the basis of the shape of their active sites.

Models, Molecular↗