Homology modeling and molecular docking for the science curriculum

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum th...

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Bibliographic Details
Published in:Biochemistry and molecular biology education 2014-03, Vol.42 (2), p.179-182
Main Authors: McDougal, Owen M., Cornia, Nic, Sambasivarao, S. V., Remm, Andrew, Mallory, Chris, Oxford, Julia Thom, Maupin, C. Mark, Andersen, Tim
Format: Article
Language:English
Subjects:
Binding Sites
Biochemistry
Biochemistry - education
College Science
computational biochemistry
Computer Simulation
Computer Software
Computer Uses in Education
Curricula
Curriculum
DockoMatic
Educational Technology
Higher education
homology modeling
Humans
Molecular Biology
molecular docking
Molecular Structure
Open source software
Protein Binding
Science education
Science Experiments
Science Instruction
Science Process Skills
Scientific Concepts
Software
Structural Homology, Protein
Undergraduate Study
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Summary:DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular structure creation, ligand binding calculations, and visualization of docking results. A student procedure is provided that illustrates the use of DockoMatic to create a homology model for the amino propeptide region (223 amino acids with two disulfide bonds) of collagen α1 (XI), followed by molecular docking of the commercial drug Arixtra® to the homology model of α1 (XI), and finally, analysis of the results of the docking experiment. The activities and Supporting Information described are intended to educate students in the use of computational tools to create and investigate homology models for other systems of interest and to train students to perform and analyze molecular docking studies. The tutorial also serves as a foundation for investigators seeking to explore the viability of using computational biochemistry to study their receptor–ligand binding motifs. © 2013 by The International Union of Biochemistry and Molecular Biology, 42(2):179–182, 2014.
ISSN:1470-8175
1539-3429
DOI:10.1002/bmb.20767