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Glossary

Here are some usefull abbreviations.

Chemoinformatics terms

Chemical Markup Language
(CML)

XML standard with special definitions for molecular structures and molecular data like spectroscopic data. The advantage of CML is the expliclite data type definition and verbosity of this format. Additionally there exists a lot of XML parsers out there which faciliate to process these data type.

Comparative Field Analysis
(ComFA)

QSAR based on grid around a molecule or a set of aligned molecules which is obtained by calculating the energy of a atom probe (often a lennard-jones potential). The with problem for this approach is the required superposition of the molecules. Topological approaches (e.g. HQSAR) can avoid this problem if we do not use 3D structures. On the otherside is it helpfull to use 3D informations make 'closer' predictions to a potentially abstract and virtual pharmacophore.

Hologram Quantitative Structure Activity Relationship
(HQSAR)

QSAR based on counted subtructure patterns. It was already shown that this approach obtains analogue results as ComFA.

Joint Commitee on Atomic and Molecular Physical Data
(JCAMP)

Format for storing chemical and physical chemical related data. Mainly used for spectroscopical data.

Maximum Common Substructure
(MCS)

This is a NP complete problem, also known as graph isomorphism. It can be efficiently solved for two molecules using clique detection algorithm.

Quantitative Structure Activity Relationship
(QSAR)

General approach to calculate a relationship between molecular structures and an experimental value, e.g. solubility. It was already shown that 2D approaches based on molecular descriptors obtains analogue results as ComFA.

Structure Based Drug Design
(SBDD)

With the structure of the target protein--ligand complex, one can better understand the structure activity relationships of existing compounds, suggest new analogs to synthesize in current series, and develop novel concepts and ideas for completely new ligand moieties. This methodology is now known as structure--based drug design.

SMiles ARbitrary Target Specification
(SMARTS)

A line notation for defining a substructure.

Simplified Molecular Input Line Entry System
(SMILES)

A line notation for defining a molecular structure.


Last changes: 08.12.2010, 16:53 CET (UTC/GMT +1 hour) wegner.
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