Computer information homology

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Kjellander, B., Masimirembwa, C.M. and Zamora, I. (2007) Exploration of enzyme-ligand interactions in CYP2D6 3A4 homology models and crystal structures using a novel computational approach. Journal of Chemical Information and Modeling, 47 (3), 1234-1247. 

The specific information present in a PSSM, even when it is made from only two or three homologous sequences, particularly favors the similarity between the sequences aligned to compute it and can improve searching sensitivity dramatically. This is because constraints on each position in a multiple alignment become better defined as more exam-... 

D descriptors are a property of the connectivity of a molecule, and hence contain little information about stereochemistry or local shape. Against that, they are easy to compute, store and manipulate. 2D descriptors have been a powerful weapon in setting up classical QSARs, perhaps because they can implicitly encode 3D features within a homologous series. 

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