Biomedical Engineering Reference
In-Depth Information
40. Israelowitz, M., Rizvi, S.W.H., Kramer, J., von Schroeder, H.P.: Computational modelling of
type I Collagen fibers to determine the extracellular matrix structure of connective tissues.
Protein Eng. Des. Sel. 18, 329-335 (2005)
41. Jacoby, S.L.S., Kowalik, J.S., Pizzo, J.T.: Interactive methods for nonlinear optimization
problems. Prentice-Hall, Englewood Cliffs (1972)
42. Tang, C.J.K., Alexandrov, V.: Relaxed Monte Carlo linear solver. In: Alexandrov, V.N.,
Dongarra, J.J., Juliano, B.A., Tan, C.J.K. (eds.) Lecture Notes in Computer Science, vol.
2073, p. 1289. Springer, Heidelberg (2001)
43. King, G., Brown, E.M., Chen, J.M.: Computer model of a bovine type I collagen microfribil.
Protein Eng. 1, 43-49 (1996)
44. Kuntz, I.D., Thomason, J.F., Oshiro, C.M.: Distance geometry. In: Openheimer N.J., James T.L.
(eds.) Methods in Enzymology, vol. 177, pp. 159-204. Academic press, New York (1989)
45. Lyngsø,
R.B.,
Pedersen,
C.N.:
RNA
pseudoknot
prediction
in
energy-based
models.
J. Comput. Biol. 7, 409-427 (2000)
46. Liu, W., Chou, K.: Prediction of protein secondary structure content. Protein Eng. 12,
1041-1050 (1999)
47. Macdonald, J.R., Johnson Jr, W.C.: Enviromental features are important in determining
protein secondary structure. Protein Sci. 10, 1172-1177 (2001)
48. Maritan, A., Micheletti, C., Triovato, A., Banava, J.B.: Optimal shapes of compact strings.
Nature 406, 287-290 (2000)
49. Marashi, S.A., Behrouzi, R., Pezeshk, H.: Adaptation of proteins to different environments: a
comparison of proteome structural properties in Bacillus subtilis and Escherichia coli.
J. Theor. Biol. 244(1), 127-132 (2007)
50. MacCallum, P.H., Poet, R., Milner-White, J.E.: Coulombic interaction between partially
charged main-chain atoms hydrogen-bonded to each other influence the confirmations of
a-helices and antiparallel b-sheet. A new method for analysing the forces between hydrogen
bonding groups in proteins includes all the coulombic interactions. J. Mol. Biol. 248,
361-373 (1995)
51. Maiti, R., von Domseleear, G.H., Zang H., Wisshart DS.: Super pose: a simple server
sophisticated structural superposition. Nucleic Acid Res. 32, W590-W594 (2004)
52. Mount, D.M.: Bioinformatics: Sequence and Genome Analysis, vol. 2. Cold Spring Harbor
Laboratory Press, Cold Spring Harbor (2004)
53. More, J.J., Wu, Z.: Issues in large scale global minimization. In: Biegler, L.T., Coleman, T. F.,
Conn, A.R., Santosa, F.N. (eds.) Large-scale optimization with applications, Part III, p. 99.
Springer-Verlag, New York (1997)
54. Morgan, D., Ceder, G., Curtarolo, S.: High-throughput and data mining with ab initio
methods. Meas. Sci. Technol. 16, 296-301 (2005)
55. Nelder, J.A., Mead, R.: A simplex method for function minimization. Comput. J. 7,
308-313 (1965)
56. Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S.,
Scheraga, H.A.: Energy parameters in polypeptides. 10. Improved geometric parameters and
nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-
containing peptides. J. Phys. Chem. 96, 6472-6484 (1992)
57. Nicholls, A., Sharp, K.A., Honig, B.: Protein folding and association: insights from the
interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991)
58. Pavanï, R., Ranghino, G.: A method to compute the volume of a molecule. Comput. Chem. 6,
133-135 (1982)
59. Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.R., Cheatham III, T.E., DeBolt, S.,
Ferguson, D., Seibe,l G., Kollman, P.: AMBER, a computer program for applying molecular
mechanics, normal mode analysis, molecular dynamics and free energy calculations to
elucidate the structures and energies of molecules. Comput. Phys. Commun. 91, 1-41 (1995)
60. Pham, T.H., Satou, K., Ho, T.B.: Support vector machines for prediction and analysis of beta
and gamma-turns in proteins. J. Bioinform. Comput. Biol. 3, 343-358 (2005)
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