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Reference List
ENM Theoretical Foundations | |
1. | Flory, P.J., Gordon, M. and McCrum, N.G. (1976) Statistical Thermodynamics of Random Networks [and Discussion]. Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences, 351, 351-380 |
2. | 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 |
3. | Haliloglu, T., Bahar, I. and Erman, B. (1997) Gaussian Dynamics of Folded Proteins. Physical Review Letters, 79, 3090-3093 |
4. | Bahar, I., Atilgan, A.R., Demirel, M.C. and Erman, B. (1998) Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability. Physical Review Letters, 80, 2733-2736 |
5. | Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O. and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J, 80, 505-515 |
6. | Tama, F. and Sanejouand, Y.H. (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng, 14, 1-6 |
Early extensions and applications | |
7. | Yang, L.W. and Bahar, I. (2005) Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure, 13, 893-904 |
8. | Ming, D. and Wall, M.E. (2005) Allostery in a coarse-grained model of protein dynamics. Phys Rev Lett, 95, 198103 |
9. | Chennubhotla, C. and Bahar, I. (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol, 3, 1716-1726 |
10. | Eyal, E. and Bahar, I. (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophys J, 94, 3424-3435 |
Recent extensions | |
11. | Li, H., Sakuraba, S., Chandrasekaran, A. and Yang, L.W. (2014) Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). J Chem Inf Model, 54, 2275-2285 |
12. | Chandrasekaran, A., Chan, J., Lim, C. and Yang, L.W. (2016) Protein Dynamics and Contact Topology Reveal Protein-DNA Binding Orientation. J Chem Theory Comput, 12, 5269-5277 |
13. | Eyal, E., Dutta, A. and Bahar, I. (2011) Cooperative dynamics of proteins unraveled by network models. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 426-439 |
14. | Yang, L.W. (2011) Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models. Biophys J, 100, 1784-1793 |
15. | Gur, M., Madura, J.D. and Bahar, I. (2013) Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophys J, 105, 1643-1652 |
Web Servers/Databases | |
16. | Lezon, T.R. and Bahar, I. (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophys J, 102, 1331-1340 |
17. | 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 |
18. | Yang, L.W., Rader, A.J., Liu, X., Jursa, C.J., Chen, S.C., Karimi, H.A. and Bahar, I. (2006) oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res, 34, W24-31 |
19. | Li, H., Chang, Y.Y., Yang, L.W. and Bahar, I. (2016) iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res, 44, D415-422 |
20. | Eyal, E., Yang, L.W. and Bahar, I. (2006) Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics, 22, 2619-2627 |
21. | Eyal, E., Lum, G. and Bahar, I. (2015) The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics, 31, 1487-1489 |
22. | Yang, L.W., Eyal, E., Bahar, I. and Kitao, A. (2009) Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics, 25, 606-614 |
23. | Bakan, A., Meireles, L.M. and Bahar, I. (2011) ProDy: protein dynamics inferred from theory and experiments. Bioinformatics, 27, 1575-1577 |
24. | Bakan, A., Dutta, A., Mao, W., Liu, Y., Chennubhotla, C., Lezon, T.R. and Bahar, I. (2014) Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics, 30, 2681-2683 |
Reviews | |
25. | Yang, L.-W., Bahar, I., Rader, A.J. and Chennubhotla, C. (2005), Normal Mode Analysis. Chapman and Hall/CRC, pp. 41-64 |
26. | Bahar, I. and Rader, A.J. (2005) Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol, 15, 586-592 |
27. | Haliloglu, T. and Bahar, I. (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol, 35, 17-23 |
28. | Bahar, I., Cheng, M.H., Lee, J.Y., Kaya, C. and Zhang, S. (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophys J, 109, 1101-1109 |
29. | Bahar, I. (2010) On the functional significance of soft modes predicted by coarse-grained models for membrane proteins. J Gen Physiol, 135, 563-573 |
30. | Bahar, I., Lezon, T.R., Bakan, A. and Shrivastava, I.H. (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev, 110, 1463-1497 |
31. | Bahar, I., Lezon, T.R., Yang, L.W. and Eyal, E. (2010) Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys, 39, 23-42 |