Parallel Flexible Molecular Docking in Computational Chemistry on High Performance Computing Clusters

  • Rafael DolezalEmail author
  • Teodorico C. Ramalho
  • Tanos C.C. França
  • Kamil Kuca
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9330)


The main objective in pharmaceutical research is development of novel drugs with improved biological effect in specifically afflicted organisms. A common practice in drug design focuses on systematic organic derivatization of chemical structures exhibiting certain biological activity and subsequent biological in vitro evaluation of the resulted benefits. However, this classical approach can be more or less classified as a chance drug discovery, being very arduous, expensive and time consuming. Nowadays, a lot of enthusiasm is given to rationally oriented drug research techniques like computer-aided drug design, virtual screening, bioinformatics, chemometrics, quantitative structure-activity relationships, etc. In the present article, we deal with designing a high performance computing (HPC) support for flexible molecular docking (FMD) which can be beneficially utilized in structure-based virtual screening (SBVS). The principles of FMD are briefly introduced and a solution combining message passing interface (MPI) with multithreading is proposed. The merits (e.g. availability, scalability, performance) of MPI-HPC enhanced SBVS/FMD are compared with other HPC techniques utilized for novel lead structures discovery in medicinal chemistry.


Molecular docking Virtual screening HPC AutoDock vina 


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Rafael Dolezal
    • 1
    • 4
    Email author
  • Teodorico C. Ramalho
    • 1
    • 2
  • Tanos C.C. França
    • 1
    • 3
  • Kamil Kuca
    • 1
    • 4
  1. 1.Faculty of Informatics and Management, Center for Basic and Applied ResearchUniversity of Hradec KrálovéHradec KrálovéCzech Republic
  2. 2.Department of ChemistryFederal University of LavrasLavrasBrazil
  3. 3.Department of ChemistryMilitary Institute of EngineeringRio de JaneiroBrazil
  4. 4.Biomedical Research CenterHradec KrálovéCzech Republic

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