MolIDE

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Developed by the Dunbrack group at Fox Chase Cancer Center, MolIDE is an open-source cross-platform program for comparative modelling of protein structures. MolIDE acts as a graphical user interface to the common tasks involved in predicting protein structures based on known homologous structures. It implements the most frequently used steps involved in modeling: secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building.

• Wang, Qiang; Canutescu, Adrian A; Dunbrack, Roland L (2008). "SCWRL and MolIDE: Computer programs for side-chain conformation prediction and homology modeling". Nature Protocols. 3 (12): 1832–47. doi:10.1038/nprot.2008.184. PMC 2682191. PMID 18989261.
• Canutescu, A. A.; Dunbrack, R. L. (2005). "MollDE: A homology modeling framework you can click with". Bioinformatics. 21 (12): 2914–6. doi:10.1093/bioinformatics/bti438. PMID 15845657.

• Dunbrack group