FAMS and FAMSBASE for Protein Structure

Hideaki Umeyama1, Mitsuo Iwadate1

1 Kitasato University, Tokyo
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 5.2
DOI:  10.1002/0471250953.bi0502s04
Online Posting Date:  February, 2004
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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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Table of Contents

  • Basic Protocol 1: Checking Famsbase for a Protein Model
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Checking Famsbase for a Protein Model

  Necessary Resources
  • Hardware
    • Any computer with an Internet connection
  • Software
    • Web browser (Internet Explorer v. 5.0 or later or Netscape v. 4.7 or later for Windows; Internet Explorer v. 4.5 or later for Macintosh)
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Figures

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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