Structural Predictions and Modeling


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


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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

ExPASy Molecular Biology Server. Provides easy‐to‐use computer graphics software for visualization of protein structures

Protein Data Bank. A collection of publicly available protein structures

Protein Structure Prediction Centre. Reviews of the CASP meetings.

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Norin, Martin(Jan 2006) Structural Predictions and Modeling. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0005732]