Abstract
The tertiary structure of proteins can reveal information that is hard to detect in a linear sequence. Knowing the tertiary structure is valuable when generating hypothesis and interpreting data. Unfortunately, the gap between the number of known protein sequences and their associated structures is widening. One way to bridge this gap is to use computer-generated structure models of proteins. Here we present concepts and online resources that can be used to identify structural domains in proteins and to create structure models of those domains.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Pacheco, B., Maccarana, M., Goodlett, DR., Malmström, A., Malmström, L. (2008), Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function. J Biol Chem 2009 Jan 16; 284(3): 1741–7.
Berman, H., Henrick, K., Nakamura, H., Markley, JL. (2007), The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35: D301–3 (pmid: 17142228).
Rohl, CA., Strauss, CE., Misura, KM., Baker, D. (2004), Protein structure prediction using Rosetta. Methods Enzymol 383: 66–93. (pmid: 15063647).
Eswar, N., Eramian, D., Webb, B., Shen, MY., Sali, A. (2008), Protein structure modeling with Modeller. Methods Mol Biol 426: 145–59. (pmid: 18542861).
Pieper, U., Eswar, N., Davis, FP., Braberg, H., Madhusudhan, MS., Rossi, A., Marti-Renom, M., Karchin, R., Webb, BM., Eramian, D., Shen, MY., Kelly, L., Melo, F., Sali, A. (2006), MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34: D291–5. (pmid: 16381869).
Simons, KT., Kooperberg, C., Huang, E., Baker, D. (1997), Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268: 209–25. (pmid: 9149153).
Das, R., Qian, B., Raman, S., Vernon, R., Thompson, J., Bradley, P., Khare, S., Tyka, MD., Bhat, D., Chivian, D., Kim, DE., Sheffler, WH., Malmström, L., Wollacott, AM., Wang, C., Andre, I., Baker, D. (2007), Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 1: 118–28. (pmid: 17894356).
Shortle, D., Simons, KT., Baker, D. (1998), Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95: 11158–62. (pmid: 9736706).
Riffle, M., Malmström, L., Davis, TN. The yeast resource center public data repository. (2005), Nucleic Acids Res 33: D378–82. (pmid: 15608220).
Kim, DE., Chivian, D., Malmström, L., Baker, D. (2005), Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins Suppl 7: 193–200. (pmid: 16187362).
Malmström, L., Riffle, M., Strauss, CE., Chivian, D., Davis, TN., Bonneau, R., Baker, D. (2007), Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5: e76. (pmid: 17373854).
Ginalski, K., Elofsson, A., Fischer, D., Rychlewski, L. (2003), 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015–8. (pmid: 12761065).
Misura, KM., Chivian, D., Rohl, CA., Kim, DE., Baker, D. (2006), Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 103: 5361–6. (pmid: 16567638).
Wetlaufer, DB. (1973), Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci USA 70: 697–701. (pmid: 4351801).
The UniProt Consortium (2008), The UniÂversal Protein Resource (UniProt) 2009. Nucleic Acids Res 2009 Jan; 37(Database issue): D169–74.
Hunter, S., Apweiler, R., Attwood, TK., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L., Finn, RD., Gough, J., Haft, D., Hulo, N., Kahn, D., Kelly, E., Laugraud, A., Letunic, I., Lonsdale, D., Lopez, R., Madera, M., Mas (2008) InterPro: the integrative protein signature database. Nucleic Acids Res 2009 Jan; 37(Database issue): D211–5.
Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, SR., Griffiths-Jones, S., Howe, KL., Marshall, M., Sonnhammer, EL. (2002), The Pfam protein families database. Nucleic Acids Res 30: 276–80. (pmid: 11752314).
Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, CJ., Hofmann, K., Bairoch, A. (2002), The PROSITE database, its status in 2002. Nucleic Acids Res 30: 235–8. (pmid: 11752303).
Gough, J., Chothia, C. (2002), SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucleic Acids Res 30: 268–72. (pmid: 11752312)
Sayle, RA., Milner-White, EJ. (1995), RASMOL: biomolecular graphics for all. Trends Biochem Sci 20: 374. (pmid: 7482707).
Kim, DE., Chivian, D., Baker, D. (2004), Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32: W526–31. (pmid: 15215442).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Malmström, L., Goodlett, D.R. (2010). Protein Structure Modeling. In: Fenyö, D. (eds) Computational Biology. Methods in Molecular Biology, vol 673. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-842-3_5
Download citation
DOI: https://doi.org/10.1007/978-1-60761-842-3_5
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-841-6
Online ISBN: 978-1-60761-842-3
eBook Packages: Springer Protocols