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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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DTome: a web-based tool for drug-target interactome construction.

Jingchun Sun¹, Yonghui Wu, Hua Xu

¹Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

BMC Bioinformatics

|August 21, 2012

Summary

DTome is a new web tool that builds drug-target networks to help researchers understand drug actions and find new drug targets. It integrates various data sources for drug discovery and toxicology.

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Area of Science:

Computational Biology
Pharmacology
Bioinformatics

Background:

Understanding drug bioactivities is critical for drug discovery, toxicology, and clinical trials.
Network pharmacology offers a promising approach to elucidate drug mechanisms.
The increasing volume of drug data necessitates automated tools for network construction.

Purpose of the Study:

To develop an automated computational workflow for constructing drug-target networks.
To create a user-friendly web-based tool, DTome (Drug-Target interactome tool), for facilitating drug discovery.

Main Methods:

Designed a computational workflow integrating data from DrugBank, PharmGKB, and PINA.
Developed DTome, a web-based tool with a database schema and interface.
DTome extracts and integrates four interaction types: adverse drug interactions, drug-target interactions, drug-gene associations, and target-/gene-protein interactions.
Included network analysis and visualization capabilities.

Main Results:

Successfully created the DTome tool for automated drug-target network construction.
DTome integrates diverse biological and chemical data sources.
Demonstrated the tool's utility with the antipsychotic drug clozapine.

Conclusions:

The DTome tool effectively investigates relationships between drugs, targets, genes, and interacting proteins.
DTome provides insights into drug action mechanisms and facilitates the identification of drug targets and adverse interactions.
The tool is publicly available to aid researchers in drug discovery and safety assessment.