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References



    AD-ENM references:

  • Zheng, W. & Doniach, S. A comparative study of motor-protein motions by using a simple elastic network model. Proc. Natl. Acad. Sci. 100, 13253-58 (2003). (pubmed)
  • Zheng, W. & Brooks, B.R. Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys. J. 89, 167-178 (2005). (pubmed)

  • Zheng, W. & Brooks, B.R. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. J. Mol. Biol. 346, 745-759 (2005). (pubmed)
  • Zheng, W., Liao, J. C., Brooks, B.R. & Doniach, S. Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins. 67, 886-96 (2007). (pubmed)

  • Zheng, W., Brooks, B.R., Doniach, S., & Thirumalai, D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure 13, 565-577 (2005). (pubmed)
  • Zheng, W., Brooks, B.R., & Thirumalai, D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc. Natl. Acad. Sci. 103, 7664-9 (2006). (pubmed)
  • Zheng, W., Brooks, B.R., & Thirumalai, D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J. (2007). (pubmed)


    • DC-ENM references:

  • Zheng, W. & Brooks, B.R. Normal modes based prediction of protein conformational changes guided by distance constraints. Biophys. J. 88, 3109-3117 (2005). (pubmed)
  • Zheng, W. & Brooks, B.R. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophys. J. 90, 4327-36 (2006). (pubmed)


    • PATH-ENM reference:

  • Zheng, W., Brooks, B.R., & Hummer, G. Protein conformational transitions explored by mixed elastic network models. Proteins (2007). (pubmed)


    • Related papers by Wenjun Zheng:

  • Zheng, W. A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations. Biophys. J. in press (2008). (pubmed)


    • If you find results from the AD-ENM server useful, please cite the above papers.


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