Igemdock: A graphical environment of enhancing gemdock using pharmacological interactions and post-screening analysis

Kai Cheng Hsu, Yen Fu Chen, Shen Rong Lin, Jinn Moon Yang

研究成果: 雜誌貢獻文章同行評審

225 引文 斯高帕斯(Scopus)

摘要

Background: Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired experimentally. Moreover, most docking programs loosely coupled the stages (binding-site and ligand preparations, virtual screening, and post-screening analysis) of structure-based virtual screening (VS). An integrated VS environment, which provides the friendly interface to seamlessly combine these VS stages and to identify the pharmacological interactions directly from screening compounds, is valuable for drug discovery.Results: We developed an easy-to-use graphic environment, iGEMDOCK, integrating VS stages (from preparations to post-screening analysis). For post-screening analysis, iGEMDOCK provides biological insights by deriving the pharmacological interactions from screening compounds without relying on the experimental data of active compounds. The pharmacological interactions represent conserved interacting residues, which often form binding pockets with specific physico-chemical properties, to play the essential functions of a target protein. Our experimental results show that the pharmacological interactions derived by iGEMDOCK are often hot spots involving in the biological functions. In addition, iGEMDOCK provides the visualizations of the protein-compound interaction profiles and the hierarchical clustering dendrogram of the compounds for post-screening analysis.Conclusions: We have developed iGEMDOCK to facilitate steps from preparations of target proteins and ligand libraries toward post-screening analysis. iGEMDOCK is especially useful for post-screening analysis and inferring pharmacological interactions from screening compounds. We believe that iGEMDOCK is useful for understanding the ligand binding mechanisms and discovering lead compounds. iGEMDOCK is available at http://gemdock.life.nctu.edu.tw/dock/igemdock.php.
原文英語
文章編號S33
期刊BMC Bioinformatics
12
發行號SUPPL. 1
DOIs
出版狀態已發佈 - 二月 15 2011
對外發佈

ASJC Scopus subject areas

  • 生物化學
  • 分子生物學
  • 電腦科學應用
  • 應用數學
  • 結構生物學

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