iGNM


NAR Molecular Biology Database Collection entry number 1850
Yang, Lee-Wei; Li, Hongchun; Chang, Yuan-Yu; Bahar, Ivet
1Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, 15213, USA
2Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300, Taiwan

Database Description

A database housing conformational dynamics data for all the proteins and their biological assemblies from PDB

Acknowledgements

We thank all staffs of iGNM 2.0 for the data collection, transformation, automation, management and software development. iGNM 2.0 is supported by the National Institutes of Health [5R01GM099738-04, 5P41GM103712-03]; and the Ministry of Science and Technology (MOST) [104-2113-M-007-019], Taiwan. We are grateful to the National Center for High-performance Computing, Taiwan, for computer time and facilities. Funding for open access charge is provided by National Institutes of Health.

References

1. Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang and Ivet Bahar (2015) iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Research. doi: 10.1093/nar/gkv1236
2. Yang,L.W., Liu,X., Jursa,C.J., Holliman,M., Rader,A.J., Karimi,H.A. and Bahar,I. (2005) iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics, 21, 2978-2987.
3. Haliloglu,T., Bahar,I. and Erman,B. (1997) Gaussian dynamics of folded proteins. Phys. Rev. Lett., 79, 3090-3093.
4. Bahar,I., Atilgan,A.R. and Erman,B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des., 2, 173-181.
5. Flory,P.J. (1976) Statistical thermodynamics of random networks. Proc. R. Soc. Lond. A., 351, 351-380.

Subcategory: Protein structure

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