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Biomedical subjects

Mathias Dunkel

Publications and source records attributed to Mathias Dunkel.

6 recordsLinked to original sources
PubMed2006

SuperHapten: a comprehensive database for small immunogenic compounds.

The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6-10% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity. SuperHapten is available online at http://bioinformatics.charite.de/superhapten.

Cross Reactions↗
PubMed2006

SuperNatural: a searchable database of available natural compounds.

Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used. The SuperNatural Database is publicly available at http://bioinformatics.charite.de/supernatural. Viewing requires the free Chime-plugin from MDL (Chime) or Java2 Runtime Environment (MView), which is also necessary for using Marvin application for chemical drawing.

Anti-Infective Agents↗
PubMed2005

SuperLigands - a database of ligand structures derived from the Protein Data Bank.

BACKGROUND: Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. DESCRIPTION: Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. CONCLUSION: SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.

Animals↗
PubMed2005

SuperDrug: a conformational drug database.

MOTIVATION: Different resources exist for experimentally determined and computed three-dimensional (3D)-structures of low molecular weight structures but for approved drugs, no free, publicly accessible source of 3D-structures and conformers is available. Furthermore, for selection purposes or for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemical (ATC) classification codes to each structure according to the WHO-scheme would be desirable. RESULTS: The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. To account for structural flexibility they are represented by 10(5) structural conformers. Here we present a web-query system enabling searches for drug name, synonyms, trade name, trivial name, formula, CAS-number, ATC-code etc. 2D-similarity screening (Tanimoto coefficients) and an automatic 3D-superposition procedure based on conformational representation are implemented. Drug structures above a similarity threshold as well as superimposed conformers can be retrieved in the mol- file format via a graphical interface. AVAILABILITY: For academic use the system is accessible at http://bioinf.charite.de/superdrug. The retrieval system requires the free browser-plugin 'chime' from MDL for visualization.

Computer Graphics↗
PubMed2005

In silico screening of drug databases for TSE inhibitors.

Today, thousands of different chemical compounds are used as drugs for a wealth of different indications. Here, we demonstrate the use of a novel conformational drug database for the search of compounds with a positive influence on Transmissible Spongiform Encephalopathies (TSEs) by using two- and three-dimensional structural similarity to compounds with known effect. Both methods are combined to deduce a list of 16 candidate drugs. The proposal of a small number of putative inhibitors out of about 2300 approved essential drugs allows testing by expensive or time-consuming methods with the advantage that all agents are well known and suitable for use in humans.

Algorithms↗