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Updated: Aug 17, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Structural study of homeodomain protein-DNA complexes using a homology modeling approach
1Theoretical Biology and Biophysics (T-10), Theoretical Division, Los Alamos National Laboratory, NM 87545, USA. cst@t10.lanl.gov
Abstract:
The homeodomain is a conserved protein motif that binds to DNA and plays a central role in gene regulation. We use homeodomain as a model system to study the specific interactions between protein and DNA in a complex. Following the fundamental concept of homology modeling, we have developed an algorithm for predicting structures of both protein and DNA using the known structure of a similar complex as the template. The accuracies of the algorithm in predicting the complex structures are evaluated when two of the homeodomain protein-DNA complexes with known structures (antennapedia and MATalpha2) are selected as test systems. This algorithm allows structural studies of homeodomain binds to DNA with different sequences.
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