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MolIDE1.6 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
- loop building
Tutorial on using MolIDE and SCWRL can be found here, Nature Protocols 3:1832-1847 (2008)
Important Notice: Announcing MolIDE1.6 (July 1, 2008):
- Easy installer for Windows version (highly recommended over Linux installation)
- One-step updating of PDB and Non-redundant protein sequence databases (both Linux and Windows)
- PSI-BLAST search of non-redundant database can be opened as a sortable table for browsing homologues of query.
- List of templates from PDB includes protein names and species.
- Works with current remediated XML files from the PDB (unannounced and undocumented changes to PDB files have caused problems in MolIDE in the last year)
- NCBI's non-redundant protein database (nr) can be replaced with Uniprot's Uniref100 database:
- Under Tools->Servers, change "NR ftp Server" to ftp.uniprot.org
- Under Tools->Servers, change "NR ftp server Path (.gz file)" to /pub/databases/uniprot/current_release/uniref/uniref100/uniref100.fasta.gz"
- Under Tools->Psiblast, change "NR Seq DB File and Path" to C:\FCCC\MolIDE\db\nr\uniref100 or wherever the uniref100 database is located
- MolIDE automatically downloads these large sequence databases (nr or uniref100) and formats them for use with BLAST.
LICENSING
MolIDE is distributed under a BSD type license:
Make sure you also license and download SCWRL and install it on your computer.
SCWRL can be obtained here.
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SCREENSHOTS
Windows ®
Click to view the full-size screen shot
Linux
Click to view the full-size screen shot
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STEREO GRAPHICS
MolIDE has also the capability of stereo3d representation (with anaglyph or shutter glasses) if used in conjunction with a regular (non quad buffered) Nvidia® video card on Microsoft Windows®. Use red/blue  anaglyph glasses to view the pictures below. You can get a free pair of glasses here.
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CONTACT
For comments, suggestions and bug reports please contact:
Qiang Wang
Roland Dunbrack
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ACKNOWLEDGEMENTS
MolIDE1.0 was written by Dr. Adrian Canutescu at Fox Chase Cancer Center.
We would like to thank the following individuals very much for their thoughtful suggestions and beta-testing:
Mike Sauder, Jonathan Arthur, Maxim Shapovalov, Cristian Dinca, Alin Constantin, Andrei Popescu, Guoli Wang, Yumi Jin, Qifang Xu, Lenka Kundrat.
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