iGNM  1.2 (Internet Accessible GNM Software)

Welcome to iGNM 1.2!  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.  To obtain the iGNM output files for PDB structures deposited after Sept 23rd 2003, please go to our online calculation server to initiate the GNM computation and generate the results. 

To begin using iGNM 1.2 simply click on one of the buttons to the left.  Instructions for how to use each section of iGNM 1.2 are provided on the pages for each component.  In order to properly view and retrieve GNM results you must have MDL CHIME and JAVA 2 Runtime Environment installed on your computer.  For a basic description of the main sections see the list below:

  • 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 results will be stored temporarily to allow you to visualize or download them from our 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:

"iGNM: A Database of Protein Functional Motions Based on Gaussian Network Model." Lee-Wei Yang, Xiong Liu, Christopher Jon Jursa, Mark Holliman, A.J. Rader, Hassan Karimi, Ivet Bahar.  Bioinformatics Jul 2005; 21: 2978 - 2987. (Full Paper)

"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.  Physical Review Letters 79, 3090-3093, 1997. (Full Paper)

Contact:

Lee-Wei Yang (about the code distribution, GNM algorithm and oGNM development)

Mark Holliman (about the new development of iGNM and website maintenance)


The T and R2 forms refer to the PDB structures deoxy-Hb and CO-bound Hb. The reconfigured T is predicted using scaling factor 4. We started from the T form and compute its most probable global change using ANM. Note the similarity between the relaxed form predicted by our computations (right) and the experimental R2 form (middle) (rms deviation 2.32 ).
 

University of Pittsburgh

School of Medicine