Tag Archives: Pfam

What’s the Answer? Lipid-binding protein database or tool?


BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question:

How to identify the lipid binding region (amino acid residues) in the protein? Any specialized online/commercial tools is there.

The first answer starts off:

You can try CGDB - a database of membrane protein/lipid interactions. You can also try the predictive algorithm for lipid-binding sites using three-dimensional structural data, described by Scott, et al.

And then continues with more to read and some description. There is (at this time) another answer using PFAM.

Updated Online Tutorials for DBTSS, Pfam and PDB

Seattle, WA (PRWEB) October 29, 2008 –  OpenHelix today announced the availability of newly updated tutorial suites on the DataBase of Transcriptional Start Sites (DBTSS), Pfam and the Protein Databank (PDB). DBTSS is a public resource for the analysis of promoter regions. Pfam is a comprehensive database of protein families manually created from multiple sequence alignments and hidden Markov models and PDB is a repository for a tremendous collection of structural information about proteins and other macromolecular structures. These three updated tutorials, in conjunction with the additional OpenHelix tutorials on ASTD, Entrez Protein and MMDB, give the researcher an excellent set of resources to carry their research from transcript to 3D protein structure.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain a  narrated, self-run, online tutorial, slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:


* to examine human promoter regions, and those in selected other species as well
* to locate transcription start sites, promoters, transcription factor binding sites and SNPs
* to use multiple query strategies to identify data of interest to your projects


* a variety of ways to search Pfam, including by keyword or by protein sequence
* how to use the information in Pfam to predict functions for uncharacterized proteins
* where you can access domain interaction data in Pfam
* about Pfam Clans, which are groups of domains from a single evolutionary origin


* how to search for structures and related information using a variety of strategies
* to understand the results pages
* how to access various tools to visualize and examine structural details

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or  visit the OpenHelix Blog for up-to- date information on genomics.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need  it. OpenHelix currently provides online self-run tutorials and on-site  training for institutions and companies on the most powerful and  popular free, web based, publicly accessible bioinformatics resources.  In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.