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Biological Sciences

Whats on this Page?

Session Goals

At the end of this session you should be able to acquire a structural perspective on the molecular basis of genetically-inherited diseases by using the following tools:

    • PubMed (Biomedical Literature) and OMIM (Online Mendelian Inheritance in Man).
       
    • Protein Data Bank or PDB for information about your protein's 3D coordinates.
       
    • PyMOL examine the effects of a mutation on protein structure and function in 3D.
       
    • Prepare and present an oral presentation on the structural and molecular basis of genetically inherited diseases.  

                                        Shortcut to this page: goo.gl/x21MXF

National Center for Biotechnology Information (NCBI)

Created in 1988, the National Centre for Biotechnology Information (NCBI) is a clearinghouse for molecular biology and genetics information. It includes links to full-text articles and numerous genetics and protein databases including the following:

  • PubMed - The place to go for the most up-to-date peer-reviewed health and life sciences journal articles. Includes over 26 million biomedical journal references dating back to the 1950's.
    (
    PubMed Tutorials)
     
  • OMIM (Online Mendelian Inheritance in Man) is a continuously updated catalogue of human genes and genetic disorders. 
    (
    OMIM Help and FAQ's-Frequently Asked Questions).



The Genetics Home Reference (Genetic Conditions) is a very useful tool for  BCEM 393  as it contains background information on genetics disorders, related genes and chromosomes.

 

PubMed

PubMed/Entrez  <--- (Use this link to connect to PubMed/Entrez)

PubMed is a Web-based retrieval system developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine. PubMed is one of the best sources for locating Biomedical articles as it includes approximately 26 million references in the health and life sciences.
 

Use PubMed to locate further background information on your disease topic.

OMIM Online Inheritance in Man

OMIM-Online Mendelian Inheritance in Man <--- Use this link to connect to OMIM )

OMIM is an updated catalogue of human genes and disorders which is maintained by a team of science writers and editors at Johns Hopkins University. OMIM is intended for physicians and other professionals researching genetic disorders and by advanced students in science and medicine.

Use OMIM to find general information on your disease topic, inheritance pattern, gene location, history, etc.
Many related PubMed references are also included.


 

Enzyme Question (See your FAQ's or Frequently Asked Questions in D2L)

To find the class that your enzyme belongs to open the following link and type in the name of your enzyme (EC# 2.7.1.1).
http://enzyme.expasy.org/

 

Link

RCSB's Protein Data Bank (PDB)

RCSB's Protein Data Bank (PDB) <--- (Use this link to connect to the Protein Data Bank (PDB)

The Research Collaboratory for Structural Bioinformatics (RCSB) manages The Protein Data Bank (PDB) which is the worldwide repository or archive of information about the 3D structures of large biological molecules, including proteins and nucleic acids. The PDB contains the three-dimensional coordinates of proteins and can be searched by protein name, keyword, PDB file name or PDB ID.
(See  Appendex A of your assignment, eg. 3GFT.pdb for the K-Ras Protein)

The three-dimensional coordinates are the coordinates for the wild-type protein. When searching the Protein Data Bank website enter your coordinate file information e.g. 3GFT in the search box, and NOT 3GFT.pdb or the example you are using for this assignment.  


 Amino Acid Abbreviations (IUPAC)
http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html

Catalytic Site Atlas-EMBL
http://www.ebi.ac.uk/thornton-srv/databases/CSA/

 

Citing Your Literature

Journal articles and websites that you have used for your assignment must be properly cited. Biochemistry 393 follows the Harvard style and consists of the following:

Author(s) of article - surname and initials. Year of publication. Title of article, Journal name - italicised or underline, volume number, issue number, page number(s).
 

Examples:

Sueblinvong, V., Suratt, B.T. and  Weiss, D.J. 2007. Novel therapies for the treatment of cystic fibrosis: new developments in gene and stem cell therapy, Clinics in Chest Medicine, 28(2), 361-379.

More than four Authors:
Bonvillian, B. et al., 2007. Post-operative infections in cystic fibrosis and non-cystic fibrosis patients after lung transplantation, The Journal of Lung and Heart Transplantation, 26(9), 890-897.

 

Anglia Ruskin University-Harvard Style Examples
http://libweb.anglia.ac.uk/referencing/harvard.htm

Contact the Biology Librarian

Any questions, suggestions or comments should be sent to Jennifer Lee, Interim Liaison Librarian for Biological Sciences, Physics, Astronomy and Mathematics

Email: jelee@ucalgary.ca
Phone: 403.220.8726
Send Email

 

Updated January 27, 2017