Relational protein database

DITOP Drug-Induced Toxicity-Related Protein Database provides information about drug-indueed toxicity associated with proteins. It includes data overdose toxicity, idiosyncratic toxicity, drug-drug interactions and genotoxicity http // bioinfxmu.edu.cn/databases/DITOP/... 

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/). 

So, back then to aspirin. Very often, X-ray data is available for the molecule of interest or related molecules. The lingua franca for molecular modelling purposes is a file of Cartesian coordinates such as the following. pdb (Protein Database) file. Figure 1.13, for aspirin. 

The application of the primary databases and structural analytical tools will be introduced using a protein from a future experiment. In Experiment 4, you will extract, purify, and characterize a-lactalbumin from bovine milk. To prepare for this activity, here you will learn about the structure of a related protein, a-lactalbumin from humans. We will search databases to find and view its primary and secondary structure and also determine if there are other proteins with a similar amino acid sequence and structure. After completion of these exercises, you will be able to apply these computer tools to proteins of your own choice. 

The EMBL in Heidelberg provides a multitude of services that can be hclprful Ah the molecular modeler. DSSF, HSSFt FSSP, FDBFINDER, PDBREPORT, and PDB SELECT are derived protein databases. They are based on data from the Protein Data Bank of 3D structures and the Swissprot database of LD protein sequences. The data and related software can be obtained vis anonymous FTP or, mote easily these days, via the WWW. 

Database searches aimed at identifying related proteins found that the closest structural relative to bacteriocin AS-48 is the effector polypeptide from porcine lymphocytes, NK-lysin.63 Similar to AS-48, this 76-residue protein adopts a globular fold with five helices surrounding a hydrophobic core but lacks a circular backbone.64 Instead, NK-lysin comprises three cross-bracing disulphide bonds that stabilise the structure. Despite the linear backbone of NK-lysin creating differences in the orientation of helix 5 in relation to the one in AS-48, and despite no significant sequence homology between them, the backbone... 

Clauser et al. 1999). However, there remain several limitations. The lack of complete and accurately annotated databases limits the quality of matches that can be achieved. The greater number of highly homologous proteins in higher organism complicates the distinguishing between closely related proteins. Last but not least, information of peptide sequences and sites of modifications cannot be deduced from PMF measurements. 

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