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
files for PDB structures deposited after Sept 23rd 2003, please go to our
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
and JAVA 2 Runtime
Environment installed on your computer. For a basic description of
the main sections see the list below:
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.
Search: Use this
section to perform a simple search of the iGNM database for retrieving and
downloading GNM output files for a specified protein.
Use this section to
compare the ribbon diagrams or 2-D plotted graphs of both Theoretical and
Experimental protein B-factors.
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.
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.
To learn about GNM and what it does,
To obtain a copy of the GNM source code for you own use,
To learn about the
types of different output files that can be generated by the GNM,
To know more about conformational dynamics of proteins,
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.
Jul 2005; 21: 2978 - 2987.
"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
"Gaussian dynamics of
folded proteins" T. Haliloglu, I. Bahar, B. Erman. Physical Review Letters 79, 3090-3093, 1997. (Full
(about the code distribution, GNM algorithm and oGNM development)
Mark Holliman (about the new development of iGNM and website