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Reference List

 

        1.    Li,H., Chang,YY, Yang,LW and Bahar,I. (2015) iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Res., published online, doi: 10.1093/nar/gkv1236

        2.    Flory,P.J. (1976) Statistical thermodynamics of random networks. Proc. R. Soc. Lond. A., 351, 351-380.

        3.    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.

        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. Phys. Rev. Lett., 80, 23.

        5.    Bahar,I. and Rader,A.J. (2005) Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol., 15, 586-592.

        6.    Rader,A.J., Chennubhotla,C., Yang,L.W. and Bahar,I. (2006) The Gaussian network model: Theory and applications. In Bahar,I. and Cui,Q. (eds.), NORMAL MODE ANALYSIS: THEORY AND APPLICATIONS TO BIOLOGICAL AND CHEMICAL SYSTEMS. Chapman & Hall/CRC: Boca Raton, FL, pp. 41-64.

        7.    Eyal,E., Dutta,A. and Bahar,I. (2011) Cooperative dynamics of proteins unraveled by network models. WIREs Comput Mol Sci, 1, 426-439.

        8.    Yang,L.W. (2011) Models with energy penalty on interresidue rotation address insufficiencies of conventional elastic network models. Biophys. J., 100, 1784-1793.

        9.   Tama,F. and Sanejouand,Y.H. (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng., 14, 1-6.

      10.   Brüschweiler,R. (1995) Collective protein dynamics and nuclear spin relaxation. J. Chem. Phys., 102, 3396-3403.

      11.    Haliloglu,T., Bahar,I. and Erman,B. (1997) Gaussian dynamics of folded proteins. Phys. Rev. Lett., 79, 3090-3093.

      12.    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.

      13.    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-W31.

      14.    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.

      15.    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.

      16.    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.