KOSMOS

Source codes

KOSMOS provides exercise codes to the public. Please refer to the manual file named "readme.pdf" in each file.
The source code is implemented on the Matlab environment.
KOSMOS is licensed under the GNU General Public License version 2.

• NMA (Normal mode analysis)
• ENI (Elastic network interpolation)
• ICONGENI (Internal coordinate normal mode-guided elastic network interpolation)

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References

1. Kim, M.K., Chirikjian, G.S., Jernigan, R.L., "Elastic Models of Conformational Transitions in Macromolecules", Journal of Molecular Graphics and Modelling, Vol. 21, pp. 151-160, 2002. [DOWNLOAD]
2. Kim, M.K., Jernigan, R.L., Chirikjian, G.S., "Efficient Generation of Feasible Pathways for Protein Conformational Transitions", Biophysical Journal, Vol. 83, pp. 1620-1630, 2002. [DOWNLOAD]
3. Kim, M.K., Li, W., Shapiro, B.A., Chirikjian, G.S., "A Comparison between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA", Journal of Biomolecular Structure and Dynamics, Vol. 21, pp. 395-405, 2003. [DOWNLOAD]
4. Kim, M.K., Jernigan, R.L., Chirikjian, G.S., "An Elastic Network Model of HK97 Capsid Maturation", Journal of Structural Biology, Vol. 143, pp. 107-117, 2003. [DOWNLOAD]
5. Kim, M.K., Jernigan, R.L., Chirikjian, G.S., "Rigid Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies", Biophysical Journal, Vol. 89, pp. 43-55, 2005. [DOWNLOAD]
6. Jeong, J.I., Jang, Y., Kim, M.K., "A Connection Rule for Alpha-Carbon Coarse-Grained Elastic Network Models Using Chemical Bond Information", Journal of Molecular Graphics and Modelling, Vol. 24, pp. 296-306, 2006. [DOWNLOAD]
7. Jang, Y., Jeong, J.I., Kim, M.K., "UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models", Nucleic Acids Research, Vol. 34, pp. W57-W62, 2006. [DOWNLOAD]
8. Kim, M.K., Jang, Y., Jeong, J.I., "Using harmonic analysis and optimization to study macromolecular dynamics", International Journal of Control, Automation, and Systems, Vol. 4, pp. 382-393, 2006. [DOWNLOAD]
9. Hu, M., Raj, S., Kim, B., Liu, W.K., Baik, S.H., Kim, T.S., Lim, B.S., Kim, M.K. "Precise spring constant assignment in elastic network model for identification of vibration frequency and modeshape", The Journal of Mechanical Science and Technology Vol. 24, no. 9 pp. 1771-1780, 2010. [DOWNLOAD]

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Computational Bioengineering Lab. School of Mechanical Engineering & Department of Nano Science and Technology
Rm 22106. Sungkyunkwan Univ. 300. Chunchun-Dong. Jangan-Gu. 440-746. Korea,
E-mail : qktndn@skku.edu