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Comparative protein structure

Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family. Figure 1 The basis of comparative protein structure modeling. Comparative modeling is possible because evolution resulted in families of proteins, such as the flavodoxin family, modeled here, which share both similar sequences and 3D structures. In this illustration, the 3D structure of the flavodoxin sequence from C. crispus (target) can be modeled using other structures in the same family (templates). The tree shows the sequence similarity (percent sequence identity) and structural similarity (the percentage of the atoms that superpose within 3.8 A of each other and the RMS difference between them) among the members of the family.
Comparative Protein Structure Modeling VIII. CONCLUSION... [Pg.301]

We are grateful to Dr. Azat Badretdinov and Mr. Eric Feyfant for many discussions about comparative protein structure modeling. AF is a Burroughs Wellcome Fellow. RS is a Howard Hughes Medical Institute predoctoral fellow. FM is a Norman and Rosita Winston Biomedical Research Foundation Fellow. AS is a Sinsheimer Scholar and an Alfred P. Sloan Research Fellow. The investigations have also been aided by grants from NIH (GM 54762) and NSF (BIR-9601845). [Pg.301]

R Sanchez, A Sail. Evaluation of comparative protein structure modeling by MODELLER-3. Pi otems Suppl 1 50-58, 1997. [Pg.304]

R Sanchez, A Sail. ModBase A database of comparative protein structure models. Biomfor-matics 15 1060-1061, 1999. [Pg.312]

Marti-Renom MA et al (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29 291-325... [Pg.372]

Sanchez, R., and Sali, A. (1997). Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7, 206-214. [Pg.274]

Sanchez R, Sali A. 1997. Advances in comparative protein-structure modeUing. Curr Opin Struct Biol 7(2) 206-214. [Pg.304]

E. Wittenstein, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2000, 28, 250-253. [Pg.247]

Sippl, M. J., On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations./ Mol Biol, 1982. 156(2) p. 359-88. [Pg.316]

Pieper, U., N. Eswar, H. Braberg, M. S. Madhusudhan, F. P. Davis, A. C. Stuart, N. Mirkovic, et al. 2004. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 32, Database Issue D217-22. [Pg.302]

R. Sanchez A. Sali, Comparative Protein Structure Modeling Introduction and Practical Examples with MODELLER In Protein Structure Prediction, Methods and Protocot D. M. Webster, Ed. Humana press Totowa, NJ, 2000 pp 97-129. [Pg.486]

Fiser A, Sanchez R, Melo F et al. Comparative protein structure modeling. Computational Biochemistry and Biophysics. New York Marcel Dekker, 2001 275-312. [Pg.115]


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