Structural Predictions and Modeling

Abstract

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

Altschul S, Madden T, Schaffen A, et al. (1997) Gapped BLAST and PSI‐BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389–3402.

Desmet J, De Maeyer M, Hasez B and Lasters I (1992) The dead‐end elimination theorem and its use in protein side‐chain positioning. Nature 356: 539–542.

Fetrow J, Siew N and Skolnick J (1999) Structure‐based functional motif identifies a potential disulphide oxidoreductase active site in the serine/threonine protein phosphatase‐1 subfamily. Federation of American Societies for Experimental Biology 13: 1866–1874.

Fiser A, Do R and Sali A (2000) Modeling of loops in protein structures. Protein Science 9: 1753–1773.

Hofmann K, Bucher P, Falquet L and Bairoch A (1999) The PROSITE database, its status in 1999. Nucleic Acids Research 27: 215–219.

Kasuya A and Thornton J (1999) Three‐dimensional structure analysis of PROSITE patterns. Journal of Molecular Biology 286: 1673–1691.

Kolinsky A, Betancourt MR, Kihara D, Rotkiewicz R and Skolnick J (2001) Generalized comparative modeling (GENECOMP): a combination of sequence comparisons, threading, and lattice modeling for protein structure prediction and refinement. Proteins 44: 133–149.

Moult J (1999) Predicting protein three‐dimensional structure. Current Opinion in Biotechnology 10: 583–588.

Murzin AG (2001) Progress in protein structure prediction. Nature Structural Biology 8: 110–112.

Ponder J and Richards F (1987) Use of packing criteria in the enumeration of allowed sequences for different structural classes. Journal of Molecular Biology 193: 775–791.

Sippl M (1990) The calculation of conformational ensembles from potentials of mean force, an approach to the prediction of local structures in globular proteins. Journal of Molecular Biology 213: 659–883.

Sowa M, He W, Slep K, et al. (2001) Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nature Structural Biology 8: 234–237.

Sternberg MJE, Bates PA, Kelley LA and MacCallum RM (1999) Progress in protein structure prediction: assessment of CASP3. Current Opinion in Structural Biology 9: 368–373.

Thompson J, Higgins D and Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.

Vitkup D, Melamud E, Moult J and Sander C (2001) Completeness in structural genomics. Nature Structural Biology 8(6): 559–566.

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 http://www.expasy.ch

Protein Data Bank. A collection of publicly available protein structures http://www.rcsb.org/pdb

Protein Structure Prediction Centre. Reviews of the CASP meetings. http://PredictionCenter.llnl.gov

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

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]