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ERIC Number: EJ1028977
Record Type: Journal
Publication Date: 2014
Pages: 4
Abstractor: As Provided
Reference Count: N/A
ISSN: ISSN-1470-8175
Homology Modeling and Molecular Docking for the Science Curriculum
McDougal, Owen M.; Cornia, Nic; Sambasivarao, S. V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim
Biochemistry and Molecular Biology Education, v42 n2 p179-182 Mar-Apr 2014
DockoMatic 2.0 is a powerful open source software program (downloadable from 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 a1 (XI), followed by molecular docking of the commercial drug Arixtra® to the homology model of a1 (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.
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Publication Type: Journal Articles; Reports - Descriptive
Education Level: Higher Education; Postsecondary Education
Audience: Teachers
Language: English
Sponsor: N/A
Authoring Institution: N/A