Analyzing and Modeling Data

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Structures, Reactions and Data Retrieval

The following section provides an overview of the capabilities of our structure and reaction search engine.

String Search

String search is the fastest method available to retrieve specific information on a compound or on a group of compounds that share similar properties such as for instance chemical formula.
Searches can be performed on the following three properties:
- CAS number
- chemical formula with or without wildcards
- chemical name with or without wildcards

Property Search

Property-based queries operate on arithmetic values and can involve conditional operators like for instance 'equal', 'greater than' or 'lower or equal to'. These conditional operators can be combined with logical operators ('or', 'and') to form sophisticated queries. The following table offers a non-exhaustive overview of molecular properties that can be queried:

Category Description

Molecular Properties - number of atoms
- molecular weight
- molecular complexity index
- total molecular and accessible surface

Atom Count - number of H-acceptors / H-donors
- number of stereocenters
- number of 'unusual' isotopes (¹³C instead of ¹²C)
- number of aromatic/non-aromatic atoms
- number of atoms with a given formal charge
- number of metal/non-metal atoms
- number of heteroatoms

Bond Count - number of rotatable bonds
- number of conjugated bonds
- number of aromatic bonds
- number of multicentered bonds

Ring Count - number of rings
- size-specific number of rings

Structure Search

Structure search is designed to retrieve compounds based on their chemical topology. This search procedure is usually linked to a chemical structure editor for easy input (i.e. drawing) of the query compound. It should be noted that each of the procedures listed below can be performed with or without explicit assignment of hydrogen atoms. Chirality can be specified or omitted.
- Exact Structure Match: is used to retrieve compounds that match the query structure. To be considered a hit, the target structure has to have at least its heavy atoms topology identical to the query structure.
- Similarity Search: is designed to retrieve compounds that have similar topology but not necessarily identical properties. The method used is based on structural fingerprints that encode the presence or absence of 458 chemical fragments. The match between query and target structure is estimated by the Tanimoto index that is derived from their fingerprints.

Precursor Search

Precursor search is used to retrieve compounds that can be transformed by common organic reactions into the query structure. 22 chemical transformations are encoded in this search method.
C@ROL structure search engine includes an innovative method for the identification of precursor material. This precursor search analyzes the chemical reactivity of the query compound to identify potential starting materials in a database of commercially available compounds. This procedure ensures that the proposed starting material can be transformed into the query structure by simple chemical reactions.
The precursor search is based on the retro-synthetic approach developed for the package WODCA.

Substructure Search

Substructure search is designed to retrieve compounds that share fragments with identical topology. The sophistication of queries ranges from 'exact fragment matching' where atom and bond types are strictly matched to 'fuzzy fragment matching' where atom and bond type are partially matched. Stereochemistry can be taken into account.

3D Pharmacophore Search

This search method allows the retrieval of compounds that share common spatial features called pharmacophore. In the context of a drug discovery project these features are usually of biological relevance like for instance negatively or positively charged atoms, aromatic rings, hydrophobic regions, etc. The relative special position of these features is considered during pharmacophore searching. The table below list the type of features and the geometrical constraints that can be assigned to them.

Category	Description
Pharmacophore features	A pharmacophore is defined by 3 properties: 1) the numbers of features considered 2) their spatial localization 3) their physicochemical properties such as: - hydrogen bond donor/acceptor, - charge, - hydrophobicity, - aromaticity
Geometric constraints	- distance between two pharmacophore features - angle defined by three pharmacophore features - torsion angle defined by four pharmacophore features

Reaction Center Search

Reaction search is specifically designed to search for molecule fragments involved in chemical reactions. This search procedure operates on reaction databases where reactants, solvents and products are stored. Queries can be designed to extract reactions based on the nature of the reactive center that undergo chemical transformation or based on substructures that are not altered by a chemical reaction. It should be noted that full structure and substructure search can also be performed on reactant, solvent or product molecules.