FlexServ help book

References

Alder B.J. and Wainwright T.E.. 1959. Studies in Molecular Dynamics. I. General Method. Journal of Chemical Physics 31, 459-466.

Amadei A, Linssen A.B.M., Berendsen H.J.C.. "Essential dynamics of proteins". Prot. Struct. Funct. Genet. (1993), 17, 412–425.

Atilgan, A. R., S. R. Durell, et al. (2001). "Anisotropy of fluctuation dynamics of proteins with an elastic network model." Biophysical Journal 80(1): 505-515.

Bahar, I., A. R. Atilgan, et al. (1997). "Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential." Fold Des 2(3): 173-81.

Brooks III, C. L., M. Karplus, et al. (1987). Proteins: A theoretical Perspective of Dynamics, Structure and Thermodynamics. Cambridge, Cambridge University Press.

Brüschweiler R.. "Collective protein dynamics and nuclear spin relaxation". J. Chem. Phys. (1995), 102(8), 3396-3403

Damm K.L. and Carlson H.A.. "Robust-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures". Biophysical Journal. (2006), 90, 4558-4573.

Ding F., Buldyrev S.V. and Dokholyan N.V. 2005. Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. Biophysical Journal 88, 147-155.

Dokholyan N.V., Buldyrev S.V., Stanley H.E. and Shakhnovich E.I.. "Discrete molecular dynamics studies of the folding of a protein-like model". Folding & Design. (1998), 3, 577-587.

Emperador A, Carrillo O, Rueda M and Orozco M. “Exploring the suitability of coarse-grained techniques for the representation of protein dynamics”. Biophysical Journal. (2008), 95, 2127-2138.

Falke J.J. "A moving story". Enzymology, Science. (2002), 295, 1480-1481.

Gardiner C.W.. "Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences". (1989), 2nd ed. Springer, Berlin.

Go, N. and H. A. Scheraga (1976). "On the Use of Classical Statistical Mechanics in the Treatment of Polymer Chain Conformation." Macromolecules 9: 535-542.

Haliloglu, T., I. Bahar, et al. (1997). "Gaussian dynamics of folded proteins." Physical Review Letters 79(16): 3090-3093.

Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M.and Kern D.. "A hierarchy of timescales in protein dynamics is linked to enzyme catalysis". Nature. (2007), 450, 913-916

Kelly L. Damm and Heather A. Carlson. "Robust-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures". Biophysical Journal. (2006), 90, 4558-4573.

Kabsch W. "A solution for the best rotation to relate two sets of vectors". Acta Crystallogr. (1976), A32:922-923.

Karplus M. and Kuriyan J.. "Molecular dynamics and protein function". Proc. Natl. Acad. Sci. (2005), 102, 6679-6685.

Kenakin T. "Agonist-receptor efficacy. I: Mechanisms of efficacy and receptor promiscuity". Trends Pharmacol. Sci. (1995), 16, 188-192.

Kovacs, J. A., P. Chacon, et al. (2004). "Predictions of protein flexibility: first-order measures." Proteins 56(4): 661-8.

Ma J. and Karplus M. "The allosteric mechanism of the chaperonin GroEL: a dynamic analysis". Proc. Natl. Acad. Sci. (1998), 95, 8502-8507.

Ma J. "Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes". Structure. (2005), 13, 373-380.

Marvin J.S. and Hellinga H.W.. "Manipulation of ligand binding affinity by exploitation of conformational coupling". Nat. Struct. Biol. (2001), 8, 795-798.

McCammon J.A., Gelin B.R. and Karplus M.. "Dynamics of folded proteins". Nature. (1977), 267, 585-590.

Meyer T, Ferrer-Costa C, Pérez A, Rueda M, Bidon-Chanal A, Luque F.J., Laughton C.A. and Orozco M. “Essential Dynamics: A Tool for Efficient Trajectory Compression and Management” J.Chem.Theor.Comput (2006) 2, 251-258.

Navizet I., Cailliez F. and Lavery R.. "Probing Protein Mechanics: Residue-Level Properties and Their Use in Defining Domains". Biophysical Journal. (2004), 87, 1426-1435

Noy A., Meyer T., Rueda M, Ferrer C, Valencia A, Pérez A, de la Cruz X, López-Bes J.M., Luque F.J. and Orozco M.. “Data mining of molecular dynamics trajectories of nucleic acids”. J.Biomol.Struct.Dynam. (2006), 23, 447-455.

Orozco M, Noy A, Meyer T, Rueda M, Ferrer C, Valencia A, Pérez A, Carrillo O, Fernández-Recio J, de la Cruz X and Luque F.J.. “Data mining of molecular dynamic trajectories of nucleic acids”. In “Computational Studies of RNA and DNA”. Challenges and Advances in Computational Chemistry and Physics. Vol 2. J.Sponer and F.Lankas (Eds). Springer. Dordrecht. 2006. pp 121-146.

Orozco M, Noy A and Pérez A. “Recent advances in the study of nucleic acid flexibility by molecular dynamics”. Curr. Op. Struct. Biol. (2008), 18, 185-193. April Front Cover Paper.

Peng S., Ding F., Urbanc B., Buldyrev S.V., Cruz L., Stanley H.E. and Dokholyan N.V.. 2004. Discrete molecular dynamics simulations of peptide aggregation. Physical Review E 69, 041908.

Rueda M, Chacón P and Orozco M. “Thorough Validation of Protein Normal Mode Analysis- A Comparative Study with Essential Dynamics”. Structure. (2007a) 15, 565-575.

Rueda M., Ferrer-Costa C., Meyer T., Perez A., Camps J., Hospital A., Gelpi J.L. and Orozco M.. "A consensus view of protein dynamics". Proc. Natl. Acad. Sci. (2007b), 104, 796-801.

Sacquin-Mora S. and Lavery R.. "Investigating the Local Flexibility of Functional Residues in Hemoproteins". Biophysical Journal. (2006), 90, 2706-2717

Sharma S., Ding F. and Dokholyan N.V. 2007. Multiscale Modeling of nucleosome dynamics. Biophysical Journal 92, 1457-1470.

Smith W.S., Hall K.C., and Freeman B.D.. 1997. Molecular dynamics for polymeric fluids using discontinuous potentials. Journal of Computational Physics 134, 16-30.

Suhre K. and Sanejouand Y.H.. 2004. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 32, W610–W614.

Tirion, M. M. (1996). "Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis." Physical Review Letters 77(9): 1905-1908.

Van Kampen N.G.. "Stochastic Processes in Physics and chemistry". (1981), North-Holland, Amsterdam.

Zhou Y, Vitkup D and Karplus M. "Native proteins are Surface-molten solids: application of the Lindemann criterion for the solid versus liquid state". J. Mol. Biol. (1999), 285(4), 1371-1375