iGNM 2.0 (Internet Accessible GNM Software)

Welcome to iGNM 2.0!  This web server hosts a database of output files obtained from running GNM calculations on PDB files and the means for visualizing these files in both 2-D and 3-D.  The iGNM database is updated every Sunday to include the latest structures added to the PDB.   Currently their are results for 52,924 structures in the iGNM database.   Customized structures can be submitted for online calculation through our oGNM server.

To begin using iGNM 2.0 simply select an option from the menus above.  Instructions for how to use each section of iGNM 2.0 are provided on the pages for each component.  In order to properly view and retrieve GNM results you must have the JAVA 2 Runtime Environment installed on your computer.  For a basic description of the main tools offered see the list below (these tools are accessible through the GNM Tools menu on the top banner).

• Mode Shapes: Use this section to view ribbon diagrams or 2-D plotted graphs of protein slow modes, fast modes, average slow modes, and average fast modes files. 

• Database Search: Use this section to perform a simple search of the iGNM database for retrieving and downloading GNM output files for a specified protein.

• B-Factors: Use this section to compare the ribbon diagrams or 2-D plotted graphs of both Theoretical and Experimental protein B-factors.  

• PDB Query: Use this section to perform a search on both the PDB and the iGNM server to locate and view .pdb files and related GNM files.

• Submit Structure: Use this section to submit your own customized structure file (obtained from comparative modeling or domain-truncated PDB files) for GNM computation.  The GNM will process your file and the results will be viewable and downloadable from the server.

GNM Links

To learn about GNM and what it does, click here.
To obtain a copy of the GNM source code for you own use, click here.
To learn about the types of different output files that can be generated by the GNM, click here.
To know more about conformational dynamics of proteins, click here.

Reference:

"Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential" I. Bahar, A.R. Atilgan, and B. Erman.  Folding & Design 2, 173-181, 1997. (Full Paper)

"Gaussian dynamics of folded proteins" T. Haliloglu, I. Bahar, B. Erman.  Biological Physical Review Letters 79, 3090-3093, 1997. (Full Paper)