Biomedical subjects

Paul Labute

Publications and source records attributed to Paul Labute.

4 recordsLinked to original sources

PubMed2004

Derivation and applications of molecular descriptors based on approximate surface area.

Three sets of molecular descriptors that can be computed from a molecular connection table are defined. The descriptors are based on the subdivision and classification of the molecular surface area according to atomic properties (such as contribution to logP, molar refractivity, and partial charge). The resulting 32 descriptors are shown (a) to be weakly correlated with each other; (b) to encode many traditional molecular descriptors; and (c) to be useful for QSAR, QSPAR, and compound classification.

Quantitative Structure-Activity Relationship↗

PubMed2002

A probabilistic approach to high throughput drug discovery.

A methodology is presented in which high throughput screening experimental data are used to construct a probabilistic QSAR model which is subsequently used to select building blocks for a virtual combinatorial library. The methodology is based upon statistical probability estimation and not regression. The methodology is applied to the construction of two focused virtual combinatorial libraries: one for cyclic GMP phosphodiesterase type V inhibitors and one for acyl-CoA:cholesterol O-acyltransferase inhibitors. The results suggest that the methodology is capable of selecting combinatorial substituents that lead to active compounds starting with binary (pass/fail) activity measurements.

3',5'-Cyclic-GMP Phosphodiesterases↗

PubMedDate not supplied

On the perception of molecules from 3D atomic coordinates.

A method is presented for perceiving chemical types of atoms in molecules given 3D atomic coordinates and element identities. The method assigns hybridizations, bond orders, and formal charges for structures whether hydrogen atoms are present. The Maximum Weighted Matching algorithm for nonbipartite graphs is used to assign bond orders with weights derived from statistics of a large collection of organic molecules. Results form tests on a collection of functional groups, heterocycles, entries from the Protein Data Bank, and Cambridge Structural Database as well as a comparison to other methods, are presented and discussed.

Algorithms↗

PubMedDate not supplied

2D structure depiction.

A comprehensive algorithm for the depiction of 2D coordinates of chemical structures is described. The methods used represent a significant improvement to the state of the art with regard to molecular connection graphs which pose particular difficulty to most layout efforts. Resulting coordinates are consistently of publication quality for a large subset of chemistry. The algorithm is discussed in detail, and measurements of its overall success are presented.

Journal Article↗