MolIDE is an open-source cross-platform graphical environment for homology modeling. It implements the most frequently used steps involved in modeling: sequence search, secondary structure prediction, multiple-round psiblast alignments, assisted alignment editing (integrating a template viewer and secondary structure prediction), side chain replacement and loop building. MolIDE takes an input target sequence and uses PSIBLAST to identify and align templates for comparative modeling of the target. The sequence alignment to any template can be manually modified within a graphical window of the target–template alignment and visualization of the alignment on the template structure. MolIDE builds the model of the target structure on the basis of the template backbone, predicted side.
- Windows / Mac OsX / Linux
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Qiang Wang, Adrian A Canutescu & Roland L Dunbrack Jr
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling
Nature Protocols 3:1832-1847 (2008)