FAMS and FAMSBASE for Protein Structure
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- Abstract
- Table of Contents
- Materials
- Figures
- Literature Cited
Abstract
The computer program FAMS (Full Automatic Modeling System) performs homology modeling of protein structures by means of an algorithm consisting of database searches and simulated annealing. FAMS produces a model in which the torsion angles of the backbone and sidechains are highly accurate. The operations of the FAMS algorithm are fully automated, and, therefore, special knowledge, techniques or experience are not required in order to obtain a biologically worthwhile protein structure.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Checking Famsbase for a Protein Model
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
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PDF or HTML at Wiley Online LibraryMaterials
Basic Protocol 1: Checking Famsbase for a Protein Model
Necessary Resources
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PDF or HTML at Wiley Online LibraryFigures
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Figure 5.2.1 Flowchart of modeling by FAMS, from sequence to structure. outlines the searching of FAMSBASE. View Image -
Figure 5.2.2 The login page of FAMSBASE. As stated on the page, one must first obtain an ID and password from an administrator of FAMSBASE. If time is a factor or one just wishes to check the contents of the database, click on the “Public login” link to go to the search page. View Image -
Figure 5.2.3 The upper part of the search page of FAMSBASE. 41 species whose genome ORFs have been determined are listed with check boxes on the left‐hand side. More details of the 41 species are described in http://spock.genes.nig.ac.jp/~gtop-old/org.html. View Image -
Figure 5.2.4 The lower part of the search page of FAMSBASE. Text boxes and radio buttons for searching the database are provided. View Image -
Figure 5.2.5 If a particular species is of interest, one may click the check boxes to the left of the species names. In this figure, Escherichia coli is selected. View Image -
Figure 5.2.6 To search the database using an ORF or protein name, input the name directly into the text box. As an example, an ORF named “abc” has been input. View Image -
Figure 5.2.7 If an amino acid sequence is of interest, input the sequence in the large text box as shown here. View Image -
Figure 5.2.8 A model list with annotations, model lengths (number of amino acids), and identity percentages of amino acid sequence alignments with experimentally known structure. To obtain a particular model, select one line by clicking on a template ID (shown in the PSIBlast column in this figure). View Image -
Figure 5.2.9 The amino acid alignment view page. To display the selected model, click the View Target button. Both the model and the template will be displayed by clicking the Superimpose button. View Image -
Figure 5.2.10 A Superimpose view using RasMol. The model is in blue and the template is in green. View Image -
Figure 5.2.11 The model viewed after clicking the View Target button. View Image -
Figure 5.2.12 The FAMS Web page. The server status is displayed in the upper right‐hand corner. View Image
Videos
Literature Cited
| Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410. | |
| Fischer, D., Elofsson, A., Rychlewski, L., Pazos, F., Valencia, A., Rost, B., Ortiz, A.R., and Dunbrack, R.L., Jr. 2001. CAFASP2: The second critical assessment of fully automated structure prediction methods. Proteins 45:171‐183. | |
| Iwadate, M., Ebisawa, K., and Umeyama, H. 2001. Comparative modeling of CAFASP2 competition. Chem‐Bio. Informatics J. 1:136‐148. | |
| Ogata, K. and Umeyama, H. 2000. An automatic homology modeling method consisting of database searches and simulated annealing. J. Mol. Graph. Model. 18:258‐272, 305‐256. | |
| Pearson, W.R. and Lipman, D.J. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85:2444‐2448. | |
| Yamaguchi, A., Iwadate, M., Suzuki, E.‐I., Yura, K., Kawakita, S., Umeyama, H., and Go, M. 2003. Enlarged FAMSBASE: Protein 3D structure models of genome sequences for 41 species. Nucleic Acids Res. 31:1‐6. | |
| Internet Resources | |
| http://physchem.pharm.kitasato-u.ac.jp/FAMS/ | |
| FAMS Web site. | |
| http://famsbase.bio.nagoya-u.ac.jp/famsbase/ | |
| FAMSBASE Web site. | |
| http://spock.genes.nig.ac.jp/~genome/gtop.html | |
| GTOP Web site. |
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