Similarity of proteins

Figure 3. Approaches to cluster protein targets for screening of small molecule libraries. Currently, protein targets are clustered based on functional or amino acid sequence similarity (left). We propose to cluster proteins purely based on structural similarity of protein cores and to apply this clustering to compound library design (right).

The presence of the regular repeated structure regions in proteins permits the comparison of their structural characteristics that display common features. A search for structural similarity of proteins can be processed at various levels of complexity depending upon the field of application. Two approaches are considered in the similarity comparison of protein sequences ... 

Yamamoto, T., Ikawa, S., Akiyama, T., Semba, K., Nomura, N., Miyajima, N., Saito, T., and Toyoshima, K. (1986). Similarity of protein encoded by the human c-erb-B-2 gene to epidermal growth factor receptor. Nature 319, 230-234. 

Zuperl, S., Pristovsek, P.. Menart, V., Gaberc-Porekar. V. and Novic, M. (2007) Chemometric approach in quantification of structural identity/similarity of proteins in biopharmaceuticals. J. Chem. Inf. Model., 47, 737—743. 

The general similarity of protein IR spectra, which requires protein spectral recognition based on weaker secondary bands or slight variations in band intensities or frequencies rather than on strong bands that are unique for each species ... 

Similarity of Proteins. When proteins are compared to find whether they are In the same group, their similarity can be tested In two aspects. One Is protein function proteins that are Identical In their catalytic functions have the same enzymatic name and EC-number given by the International Union of Biochemistry (lUB). The other way of grouping Is based on amino acid sequence. Proteins of similar sequences are classified Into the same group. 

Maggiora GM, Rohrer DC, Mestres J (2001) Comparing protein structures a Gaussian-based approach to the three-dimensional structural similarity of proteins. J Mol Grr h Model 19 168-178... 

The analysis of structural and functional similarities of proteins (Rossmann and Argos, 1976,1977,1980 Ohlsson et a/., 1974 Haber and Koshland, 1970) indicates a great conservation of three-dimensional structure which is not necessarily supported by sequence homologies. Comparison of sequences and three-dimensional structures in different families of proteins, might explain (1) why certain amino acids of the sequence are constant during evolution, (2) what the necessary requirements are to insure similarities in three-dimensional structure, and (3) what the minimum requirements are to determine and to conserve a definite function. 

Yamamoto T, Ikawa S, AkiyamaT, etal. Similarity of protein encoded by the human c-erbB-2 gene to the epidermal growth factor receptor. Nature 1986 319 ... 

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