November 9, 2009

CDD: Database for Interactive Domain Family Analysis

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 8:30 am
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Protein domains may be viewed as units in the molecular evolution of proteins and can be organized into an evolutionary classification. The set of protein domains characterized so far appears to describe no more than a few thousand superfamilies, where members of each superfamily are related to each other by common descent. Computational annotation of protein function is generally obtained via sequence similarity: once a close neighbor with known function has been identified, its annotation is copied to the sequence with unknown function. This strategy may work very well in functionally homogeneous families and when applied only for very close neighbors or suspected orthologs, but it is doomed to fail often when domain or protein families are sufficiently diverse and when no close neighbors with known function are available.

NCBI’s conserved domain database (CDD) attempts to collate that set and to organize related domain models in a hierarchical fashion, meant to reflect major ancient gene duplication events and subsequent functional diversification. The conserved domain database (CDD) is part of NCBI’s Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez.CDD provides a strategy toward a more accurate assessment of such neighbor relationships, similar to approaches termed ‘phylogenomic inference. CDD acknowledges that protein domain families may be very diverse and that they may contain sets of related subfamilies.

In CDD curation, we attempt to detect evidence for duplication and functional divergence in domain families by means of phylogenetic analysis. We record the resulting subfamily structure as a set of explicit models, but limit the analysis to ancient duplication events—several hundred million years in the past, as judged by the taxonomic distribution of protein sequences with particular domain subfamily footprints. CDD provides a search tool employing reverse position-specific BLAST (RPS–BLAST), where query sequences are compared to databases of position-specific score matrices (PSSMs), and E-values are obtained in much the same way as in the widely used PSI-BLAST application.

CDD is hosted here:





September 16, 2009

Database for Protein Protein Interactions

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 1:28 pm
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Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. These molecules are of great importance because of the function they perform.

Protein associations are studied from the perspectives of biochemistry, quantum chemistry, molecular dynamics, signal transduction and other metabolic or genetic/epigenetic networks. Protein-protein interactions are at the core of the entire Interactomics system of any living cell.These interactions involve not only the direct-contact association of protein molecules but also longer range interactions through the electrolyte, aqueous solution medium surrounding neighbor hydrated proteins over distances from less than one nanometer to distances of several tens of nanometers. Furthermore, such protein-protein interactions are thermodynamically linked functions of dynamically bound ions and water that exchange rapidly with the surrounding solution by comparison with the molecular tumbling rate (or correlation times) of the interacting proteins.

The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality Protein Protein Interaction data collected from the scientific literature by expert curators.The content is based on published experimental evidence that has been processed by human expert curators. MIPS provides the full dataset for download and a flexible and powerful web interface for users with various requirements.

Click here to access MIPS:

September 14, 2009

Protein Mutant Database: An Introduction

Filed under: Bioinformatics,Computational Biology,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 7:41 am
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Protein structure is one of the most important and popular research topics in todays era. Reaesrch on protein structure, sequence and organization gives a broad view of its functionality.

Compliations of protein mutant data are valuable as a basis for protein engineering. They provide information on what kinds of functional and/or structural influences are brought about by amino acid mutation at a specific position of protein. The Protein Mutant Database (PMD) which is being constructed covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants.

Click here to know more on PMD:

August 8, 2009

What is Kiosk Viewer ?

Filed under: Bioinformatics,Proteomics — Biointelligence: Education,Training & Consultancy Services @ 2:00 am
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Want to study protein s and their structures ?? Want to have an insight of the chosen protein structure ?? Then Kiosk Viewer is the right tool for you.

The Molecules in Motion Kiosk Viewer is a full-screen animation program that displays structures from different angles and perspectives, and focuses on chemical components within the structure. The Kiosk Viewer can be launched for any structure from the “Other Viewers” menu on the structure summary page, in PDB.

Here is a screenshot of the summary page from where Kiosk can be accessed.

Access Molecules in Motion using Kiosk Viewer

The Kiosk program runs on Mac, Windows and some versions of Linux (i.e. CentOS 5) only, and requires the latest version of Java. The program automatically downloads coordinate files into a folder, which lets users run Kiosk on an offline computer.

Here is a screen shot for the same.

A screenshot of 1KYSK protein Molecule in Kiosk Viewer

To customize the list of structures displayed in Kiosk, right click on the Kiosk Viewer link and save the file with a new name (with the .jnlp extension), for example myFavorites.jnlp. Edit the PDB IDs listed in the file and save it. Double click to launch Kiosk Viewer; press the Esc key to exit Kiosk Viewer.

To access Kiosk Viewer, follow this link: