MolIDE1.7 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 MolIDE1.7 (May 1, 2010):
Some changes in xml2pdb, blastpgp, and formatdb to deal with changes in the PDB and in Uniref and NCBI files.
On some Windows systems, there may be a problem with formatting large databases like nr and uniref100.
The program formatdb.exe splits large databases into multiple files, e.g. nr.00, nr.01, nr.02, etc.
The program creates a file with the extension .pal, such as nr.pal, that lists the individual files, nr.00, nr.01, etc.
On some systems, the .pal includes full pathnames for the list of files, e.g. C:\FCCC\MolIDE\db\nr\nr.00.pin. This causes an error on Windows when running blast. To fix this problem, remove the pathname and leave only the filenames, nr.00.pin, etc.
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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