Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows

  • K. S. Machado
  • E. K. Schroeder
  • D. D. Ruiz
  • O. Norberto de Souza
Conference paper

DOI: 10.1007/978-3-540-73731-5_1

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4643)
Cite this paper as:
Machado K.S., Schroeder E.K., Ruiz D.D., Norberto de Souza O. (2007) Automating Molecular Docking with Explicit Receptor Flexibility Using Scientific Workflows. In: Sagot MF., Walter M.E.M.T. (eds) Advances in Bioinformatics and Computational Biology. BSB 2007. Lecture Notes in Computer Science, vol 4643. Springer, Berlin, Heidelberg

Abstract

Computer assisted drug design (CADD) is a process involving the execution of many computer programs, ensuring that the ligand binds optimally to its receptor. This process is usually executed using shell scripts which input parameters assignments and result analyses are complex and time consuming. Moreover, receptors and ligands are naturally flexible molecules. In order to explicitly model the receptor flexibility during molecular docking experiments, we propose to use different receptor conformations derived from a molecular dynamics simulation trajectory. This work presents an integrated scientific workflow solution aiming at automating molecular docking with explicit inclusion of receptor flexibility. Enhydra JAWE and Shark software tools were used to model and execute workflows, respectively. To test our approach we performed docking experiments with the M. tuberculosis enzyme InhA (receptor) and three ligands: NADH, IPCF and TCL. The results illustrate the effectiveness of both the proposed workflow and the implementation of the docking processes.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • K. S. Machado
    • 1
  • E. K. Schroeder
    • 1
  • D. D. Ruiz
    • 1
  • O. Norberto de Souza
    • 1
  1. 1.Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO, Programa de Pós-Graduação em Ciência da Computação, Faculdade de Informática, PUCRS, Porto Alegre, RSBrasil

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