Class Descriptions

Locating Protein Information

This workshop will introduce a variety of databases and tools for protein information retrieval, including:

• HSLS Molecular Biology search system: search.HSLS.MolBio provides quick access to the major bioinformatics databases, software tools, and related literature on the Web, in addition to HSLS-supported license-based resources
• NCBI Entrez search system:
• Protein: a database of protein sequence records
• BLink: a program that displays the results of BLAST searches that have been done for every protein sequence in the Entrez Protein data domain
• CDD: a collection of sequence alignments and profiles representing protein domains conserved in molecular evolution (Conserved Domain Database)
• OMIN: a catalog of human genes and genetic disorders
• MMDB: a database of three-dimensional structures obtained from the Brookhaven Protein Databank (PDB), exluding theoretical models (Molecular Modeling DataBase)
• UniProt:: a comprehensive catalog of information on proteins (Universal Protein Resource); the central repository of protein sequence and function created by combining the information contained in Swiss-Prot, TrEMBL, and PIR
• HPRD: the Human Protein Reference Database; contains curated information on human proteins, including their sequenes, post-translational modifications, and interactions with other proteins
• STRING: the Search Tool for the Retrieval of INteracting Genes/proteins; a database of known and predicted protein-protein interactions
• InterPro Scan: a tool that combines different protein recognition methods into one resource; scans a given protein sequence against the protein signatures of the InterPro member databases (PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMMs)
• HSLS-licensed protein-centric databases:
• BioBase Knowledge Library, including TRANSFAC
• Ingenuity Pathways Analysis

Participants will learn how to answer questions like:

• What is the protein reference sequence(s) for EGFR?
• How many splice variants have been reported for the human EGFR gene?
• What is the molecular weight for the human muscle protein, Titan?
• What is the secondary structure of PLCg1 (PDB=1QAT)?
• What are the interaction partners for human BRCA1?

This class is approved for AMA Category 2 CME credit.

If you have questions, contact the HSLS Molecular Biology Information Service:

• Ansuman Chattopadhyay, PhD (ansuman@pitt.edu, 412-648-1297)
• Carrie Iwema, PhD, MLS (iwema@pitt.edu, 412-383-6887)

Class PowerPoint Presentation