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Homology modeling and molecular docking for the science curriculum
Author(s) -
McDougal Owen M.,
Cornia Nic,
Sambasivarao S. V.,
Remm Andrew,
Mallory Chris,
Oxford Julia Thom,
Maupin C. Mark,
Andersen Tim
Publication year - 2013
Publication title -
biochemistry and molecular biology education
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.34
H-Index - 39
eISSN - 1539-3429
pISSN - 1470-8175
DOI - 10.1002/bmb.20767
Subject(s) - docking (animal) , homology modeling , computational biology , visualization , computer science , homology (biology) , chemistry , biochemistry , amino acid , biology , artificial intelligence , enzyme , medicine , nursing
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.