Protein Sequence Analysis server

P Briffeuil, G Baudoux, C Lambert, X De Bolle, C Vmals, E Feytmans, E Depiereux. Comparative analysis of seven multiple protein sequence alignment servers Clues to enhance reliability of predictions. Biomformatics 14 357-366, 1998. 

The method of Rost and Sander (Rost and Sander, 1993), which combines neural networks with multiple sequence alignments known as PHD, is available from the PredictProtein (Rost, 1996) server of Columbia University (http //cubic.bioc. columbia.edu/predictprotein/). This Web site offers the comprehensive protein sequence analysis and structure prediction (Figure 12.8). For the secondary structure prediction, choose Submit a protein sequence for prediction to open the submission form. Enter e-mail address, paste the sequence, choose options, and then click the... 

The expasy server [33] offers references to many Web sites for protein sequence analysis and secondary structure prediction. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

The Protein Data Bank (PDB) is the primary structure database serving as the international repository for the processing and distribution of 3D structures of biomacromolecules (Bernstein et al, 1977). The database is operated by the Research Collaboratory for Structural Bioinformatics (RCSB) and is accessible from the primary RCSB site at http //www.rcsb.org/pdb/ (Berman et al., 2000). Most of the structure fold/motif/domain databases (Conte et al., 2000) and analysis servers (Brenner et al, 2000 Hofmann et al, 2000 Kelley et al., 2000 Shi et al., 2001) utilize 3D-structure information from PDB and sequence information from primary sequence databases. Some of these databases/analysis servers and their URL are listed in Table 12.3. 

ExPASy Proteomics web-server for the analysis of protein sequences and structures 166 www.expasy.org... 

PredictProtein Protein structure analysis Automatic sequence alignment, protein fold recognition, and secondary structure prediction web server 177 www.embl-heidelberg.de/predictprotein/... 

Two more examples of PTM databases are O-GLYCBASE [67], a database of O-glycosylated proteins (http //www.cbs.dtu.dk/databases/OGLYCBASE/), and PhosphoBase [68], a database of phosphorylation sites in proteins and peptides (http //www.cbs.dtu.dk/databases/PhosphoBase/). Both databases are maintained by the Center for Biological Sequence Analysis (CBS) in Denmark, which also provides prediction servers for both types of modifications (NetOGlyc and NetPhos). 

The analysis highlights a charge swap within two subgroups of the sequences, correctly predicting the presence of a salt bridge in the native folded protein (Huber et al., 1990). The AMAS program may either be downloaded and run locally, or a subset of its options can be accessed over the Web at a server hosted by EBl. 

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