Homology modeling tools

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Homology modeling is a technique used to generate a three-dimensional structural model of a protein from its amino acid sequence. Modeller is a popular software program used for homology modeling that automates model building from a sequence-structure alignment using a known protein structure as a template. Homology modeling is useful for predicting protein structure and function when experimental structures are not available.

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INTRODUCTION. NCBI. EMBL. DDBJ. CONCLUSION. REFERENSE. The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper. The NCBI houses a series of databases relevant to biotechnology and biomedicine. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature. All these databases are available online through the Entrez search engine.

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Secondary structure prediction has been around for almost a quarter of a century. The early methods suffered from a lack of data. Predictions were performed on single sequences rather than families of homologous sequences, and there were relatively few known 3D structures from which to derive parameters. Probably the most famous early methods are those of Chou & Fasman, Garnier, Osguthorbe & Robson (GOR) and Lim. Although the authors originally claimed quite high accuracies (70-80 %), under careful examination, the methods were shown to be only between 56 and 60% accurate (see Kabsch & Sander, 1984 given below). An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method. Some good references on the subject:

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