[1]
|
Chua, K.H., et al. (2006) Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody. Bioinformation, 1, 118-120.
|
[2]
|
Blundell, T.L. and Srinivasan, N. (1996) Symmetry, stability, and dynamics of multidomain and multicomponent protein systems. Proceedings of National Academy of Sciences of the USA, 93, 14243-14248.
doi:10.1073/pnas.93.25.14243
|
[3]
|
Katchalski, K., Katzir, E., Shariv. I., et al. (1992) Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques. Proceedings of National Academy of Sciences of the USA, 89, 2195-2199.
|
[4]
|
Wu, S. and Zhang, Y. (2009) Chapter 11: Protein structure prediction. In: D. Edwards, et al., Eds., Bioinformatics: Tools and Applications, Springer Science+Business Media, LLC, Berlin, 225-242.
|
[5]
|
Janin, J., Henrick, K., Moult, J., et al. (2003) A critical assessment of predicted interactions. Proteins: Structure, Function, and Bioinformatics, 52, 2-9.
doi:10.1002/prot.10381
|
[6]
|
Ramachandran, G.N., Ramakrishnan, C. and Sasisekharan, V. (1963) Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95-99.
doi:10.1016/S0022-2836(63)80023-6
|
[7]
|
Eisenberg, D., Lüthy, R. and Bowie, J.U. (1997) VERIFY3D: Assessment of protein models with three-dimensional profile. Methods in Enzymology, 277, 396-404.
doi:10.1016/S0076-6879(97)77022-8
|
[8]
|
Sanchez, R. and Sali, A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proceedings of National Academy of Sciences of the USA, 95, 13597-13602. doi:10.1073/pnas.95.23.13597
|
[9]
|
Dlakic, M. (2002) A model of the replication fork blocking protein Fob1p based on the catalytic core domain of retroviral integrates protein. Protein Science, 11, 1274-1277.
|
[10]
|
Marti-Renom, M.A., Stuart, A.C., Fiser, A., et al. (2000) Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291-325.
doi:10.1146/annurev.biophys.29.1.291
|
[11]
|
Madhusudhan, M.S., et al. (2006) Variable gap penalty for protein sequence-structure alignment. Protein Engineering, Design and Selection, 19, 129-133.
doi:10.1093/protein/gzj005
|
[12]
|
Sanchez, R., Pieper, U., Melo, F., et al. (2000) Protein structure modeling for structural genomics. Nature Structural Biology, 7, 986-990.
|
[13]
|
Colovos, C. and Yeates, T.O. (1993) Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Science, 2, 1511-1519.
doi:10.1002/pro.5560020916
|
[14]
|
Hatem, R., Pierre, B., Elie, E., et al. (2005) Structural and functional analysis of the C-terminal STAS (sulfate transporter and anti-sigma antagonist) domain of the Arabidopsis thaliana sulfate transporter SULTR. The Journal of Biological Chemistry, 280, 15976-15983.
|
[15]
|
Fiser, A., Sanchez, R., Melo, F., et al. (2001) Comparative protein structure modeling. In: Becker, O.M., Ed., Computational Biochemistry and Biophysics, Marcel Dekker, New York, 275-312.
|
[16]
|
Bowie, J.U., Luthy, R. and Eisenberg, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
doi:10.1126/science.1853201
|
[17]
|
Lüthy, R., Bowie, J.U. and Eisenberg, D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85. doi:10.1038/356083a0
|
[18]
|
Tyndall, D.A., Linda, A., Fothergill-Gilmore, P., et al. (2000) Crystal structure of a thermostable lipase from Bacillus stearohermophilus P1. Journal of Molecular Biology, 323, 859-869.
|
[19]
|
Bernstein, F.C., Koetzle, T.F., Williams, J.B., et al. (1977) Protein data bank: A computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112, 535-542. doi:10.1016/S0022-2836(77)80200-3
|
[20]
|
DeBartolo, J., Colubri, A., Jha, A.K., et al. (2009) Mimicking the folding pathway to improve homology free protein structure prediction. Proceedings of National Academy of Sciences of the USA, 106, 3734-3739.
|
[21]
|
Laskowski, R.A., Moss, D.S. and Thornton, J.M. (1993) Main-chain bond lengths and bond angles in protein structures. Journal of Molecular Biology, 231, 1049-1067.
|
[22]
|
Vriend, G. (1990) WHATIF: A molecular modeling and drug design program. Journal of Molecular Graphics, 8, 52-56. doi:10.1016/0263-7855(90)80070-V
|
[23]
|
Ryan, D., Xiaotao, Q., Rosemarie, S., et al. (2011) Relative packing groups in template-based structure prediction: Cooperative effects of true positive constraints. Journal of Computational Biology, 18, 17-26.
|