Structural Predictions and Modeling

Martin Norin, Biovitrum AB, Stockholm, Sweden

Published online: January 2006

DOI: 10.1038/npg.els.0005732

Computer models form the basis for the predictions of the molecular three-dimensional structures of polypeptides – the proteins. The different models all use the polypeptide amino acid sequence as the starting point for the prediction.

Keywords: protein structure; prediction; fold recognition; ab initio; protein function

 References
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 Further Reading
    Fetrow J, Godzik A and Skolnick J (1998) Functional analysis of the Escherichia coli genome using the sequence-to-structure- to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. Journal of Molecular Biology 281: 949–968.
    Looger L and Helliga H (2000) Generalized dead-end elimination algorithms make large-scale protein side-chain prediction tractable: implications for protein design and structural genomics. Journal of Molecular Biology 307: 429–445.
    Madej T, Boguski M and Bryant S (1995) Threading analysis suggests that the obese gene product may be a helical cytokine. FEBS Letters 373: 13–18.
    Mendes J, Nagarajaram H, Soares C, Blundell T and Carrondo M (2001) Incorporating knowledge-based biases into an energy-based side-chain modeling method: application to comparative modeling of protein structure. Biopolymers 59: 72–86.
    Norin M and Sundström M (2002) Structural proteomics: developments in structure-to-function predictions. Trends in Biotechnology 20: 79–84.
    Panchenko A, Marchler-Bauer A and Bryant S (2000). Combination of threading potentials and sequence profiles improves fold recognition. Journal of Molecular Biology 296: 1319–1331.
    Sánches R, Pieper U, Melo F, et al. (2000) Protein structure modeling for structural genomics. Nature Structural Biology 7(supplement): 986–990.
    Todd A, Orengo C and Thornton J (2001) Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology 307: 1113–1143.
    Wilson C, Kreychman J and Gerstein M (2000) Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. Journal of Molecular Biology 297: 233–249.
 Web Links
    ePath ExPASy Molecular Biology Server. Provides easy-to-use computer graphics software for visualization of protein structures http://www.expasy.ch
    ePath Protein Data Bank. A collection of publicly available protein structures http://www.rcsb.org/pdb
    ePath Protein Structure Prediction Centre. Reviews of the CASP meetings. http://PredictionCenter.llnl.gov

Related Sub-Topics:

Protein Structure | Protein Folding, Evolution and Degradation | Techniques and Tools in Molecular Biology | Computational Molecular Biology | Proteins: Structure, Function, Metabolism
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Article Title: Structural Predictions and Modeling
 
How to Cite close
Norin, Martin(Jan 2006) Structural Predictions and Modeling. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005732]