Bioinformatics with protein sequence

SPINE database software

SPINE (Structural Proteomics in the NorthEast) is the NESG's project coordination database.
The SPINE data model closely mirrors the current pepcDB data model with database tables responsible for tracking target, construct, expression, purification, X-Ray and NMR structure data. Spine generates weekly targetDB and pepcDB data depositions which are retrieved by the PSI-KB, generates meta-data required for archiving NESG constructs at the PSI-MR, and provides key NESG protein production pipeline, sample distribution, and structure determination statistics.

SPINE's Protein Sample Tube (PST) records provide detais about NESG protein samples and link into the samples target, construct, expression, purification, and structure screening SPINE records.

SPINE provides Bioinformatics information based on the protein sequences, including:

1. link to Uniprot page for each target protein
2. Pxs to predict protein crystallography success
3. predict signal peptide with signalp
4. DisMeta - (www-nmr.cabm.rutgers.edu/bioinformatics/disorder) disorder and secondary structure prediction
5. PROF PHD prediction of secondary structure(Burhard Ross Lab, Columbia University)
   
6. ZincFinder
7. Competition report to see if any homologous structures are on hold or released in the PDB and to check on the progress of any homologous sequences in the TargetDB. The target passes competition analysis if ???

Web based servers for sequence analysis:

• PredictProtein
  PredictProtein is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function. You may want to save the Predictprotein results on the local disk, because after a few days they will delete the files from their data base. Registration is free.

• ExPASy Proteomics Server
  The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures.

• Pfam database
  The Pfam database is a large collection of protein families and hidden Markov models. For each family you can:
  • Look at multiple alignments.
  • View protein domain architectures.
  • Examine species distribution.
  • Follow links to other databases.
  • View known protein structures.