Protein Structure Analysis Using Bioinformatics

There is a considerable impetus to predict accurately protein structures from sequence information because of the protein sequence/structure deficit as a consequence of the genome and full-length cDNA sequencing projects. The molecular mechanical (MM) approach to modeling of protein structures has been discussed in section 9.2, and the protein secondary structure prediction from sequence by statistical methods has been treated in section 9.5. The prediction of protein structure using bioinformatic resources will be described in this subsection. The approaches to protein structure predictions from amino acid sequences (Tsigelny, 2002 Webster, 2000) include  

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PROTEIN STRUCTURE ANALYSIS USING BIOINFORMATICS 619 Sensitive Search 1D/2D/3P Compatibility,... 

Parks, D S. Lee, D. Bolser, M. Schroeder, M. Lappe D. Oh, and J. Bhak. 2006. Comparative interactomics analysis of protein family interaction networks using PSIMAP(protein structural interactome map). Bioinformatics 21, 3234-3240. Peri, S. et al. 2003. Development of humanprotein reference database as an initial platform for approaching system biology in humans. Genome Res. 13, 2363-2371. 

The computer has become an essential tool in biochemical research. A computer may be used for the routine jobs of word processing and data collection and analysis. In addition, if a computer is connected to the Internet, then it may be used for biochemical literature searching, accessing information about nucleic acid and protein sequences, predicting protein structure, and seeking research methodology. In this experiment, students will be introduced to all of these skills in bioinformatics. 

The terms bioinformatics and cheminformatics refer to the use of computational methods in the study of biology and chemistry. Information from DNA or protein sequences, protein structure, and chemical structure is used to build models of biochemical systems or models of the interaction of a biochemical system with a small molecule (e.g., a drug). There are mathematical and statistical methods for analysis, public databases, and literature associated with each of these disciplines. However, there is substantial value in considering the interaction between these areas and in building computational models that integrate data from both sources. In the most... 

The computational approaches to predict protein structures from their amino acid sequences can be either empirical or knowledge-based. The former involves calculations of the energetically favorable structures by the use of the parameterized force fields (section 9.2) and the latter performs statistical analysis with references to the existing structures employing ranges of bioinformatic techniques (section 16.5). The comparative structural analysis leads to homologous models, which are then refined by energy minimization. 

Bioinformatics is a relatively new discipline that is concerned with the collection, organisatic and analysis of biological data. It is beyond our scope to provide a comprehensive overvie of this discipline a few textbooks and reviews that serve this purpose are now available (s the suggestions for further reading). However, we will discuss some of the main rnethoc that are particularly useful when trying to predict the three-dimensional structure and fum tion of a protein. To help with this. Appendix 10.1 contains a limited selection of some of tf common abbreviations and acronyms used in bioinformatics and Appendix 10.2 lists sorr of the most widely used databases and other resources. 

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