Protein selectivity index

As a result of the en2ymatic degradation of proteins, key indexes change, ie, protein solubiUty indexes (PSI), peptide chain length (PCL), and protein solubihty in 0.8 Af TCA (TCA-index) (Fig. 14). Unpleasant bitterness was once a problem for some protein hydroly2ates. This problem can now be overcome by proper selection of the reaction parameters and the en2ymes used. 

It is fortunate that theory has been extended to take into account selective interactions in multicomponent systems, and it is seen from Eq. (91) (which is the expression used for the plots in Fig. 42 b) that the intercept at infinite dilution of protein or other solute does give the reciprocal of its correct molecular weight M2. This procedure is a straightforward one whereby one specifies within the constant K [Eq. (24)] a specific refractive index increment (9n7dc2)TiM. The subscript (i (a shorter way of writing subscripts jUj and ju3) signifies that the increments are to be taken at constant chemical potential of all diffusible solutes, that is, the components other than the polymer. This constitutes the osmotic pressure condition whereby only the macromolecule (component-2) is non-diffusible through a semi-permeable membrane. The quantity... 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

The NCBI s Entrez is apowerful database search engine. This integrated search engine provides a menu (http //www.ncbi.nih.gov/Entrez/index.html) offering the user selections to search biomedical literature (PubMed), databases on OMIM, nucleotide sequence, protein sequence, whole genome sequences, 3D macromolecular structures, taxonomy (organisms in GenBank), SNP,... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

Comparative analysis of the performance of various algorithms has been carried out in the past (Kabsh and Sander, 1983). However, this task can be deceptive if factors such as the selection of proteins for the testing set and the choice of the scoring index are not carried out properly. The present work alms to provide an updated evaluation of several predictive methods with a testing set size that permits to obtain more accurate statistics, which in turn can possibly measure the usefulness of the information gathered by those methods and also identify trends that characterize the behavior of individual algorithms. Further, we present a uniform testing of these methods, vis-a-vis the size of the datasets, the measure of accuracy and proper cross-validation procedures. 

The first step in the analysis was to obtain the secondary structure prediction for the 148 proteins in the test database with the selected methods. The accuracy results in terms of the Q3 index can be examined in table III. 

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