Modeling of protein structures

S. Sun, Reduced representation model of protein structure prediction statistical potential and genetic algorithms. Protein Sci. 2 (1993), 762-785. 

CM Topham, A McLeod, E Eisenmenger, JP Overmgton, MS Johnson, TL Blundell. Erag-ment ranking in modelling of protein structure. Conformationally constrained environmental ammo acid substitution tables. J Mol Biol 229 194-220, 1993. 

P Koehl, M Delame. A self consistent mean field approach to simultaneous gap closure and side-chain positioning m protein homology modelling. Nature Struct Biol 2 163-170, 1995. R Samudrala, J Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 279 287-302, 1998. 

The aim of the second dimension depth is to consider protein 3D-stmctures to uncover structure-function relationships. Starting from the protein sequences, the steps in the depth dimension are structure prediction, homology modeling of protein structures, and the simulation of protein-protein interactions and ligand-complexes. 

Schueler-Furman O et al (2005) Progress on modeling of protein structures and interactions. Science 310(5748) 638-642... 

Figure 4 Steps in homology modeling of protein structure. Modeling the structure of a protein by considering its homology to known homologs is one of the most effective methods of structure-prediction. The critical steps are the identification and alignment of the target sequence to the template sequence (1) and (2).

Most comprehensive software programs suitable for protein modeling are commercial packages, some of which are listed in Table 15.2. The application of HyperChem in the biomolecular modeling has been described (Chapter 14) and can be extended to the modeling of protein structures. The aspects of protein modeling will be illustrated with two freeware programs and two online servers. 

The first resources for computer modeling of protein structure are the nucleic acid and protein sequence databases (see Table 6.1), curated by the European Molecular Biology Laboratory (EMBL) in Europe, the National Center for Biotechnology Information (GenBank at the NCBl) in the United States, and the DNA Database of Japan (DDBJ) in Japan. These databases are accessible via the Internet, and most likely one s own scientific institution maintains a local version, which is updated through CD-ROMs released quarterly. Perhaps the predominant protein sequence database is SWISS-PROT. - Others include the nonredundant protein sequence database (OWL) and the protein identification resource database (PIR). ... 

R. Samudrala, J. Moult. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol. 1998, 279, 287-302. 

Zimmer, R. and J. Halfmann, Optimizing Homology Models of protein structures with potentials of mean force, in Monte Carlo Approach to Biopolymers and protein Folding, P. B. Grassberger, G., Nadler, W., Editor. 1998, World Scientific, p. 45-68. 

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