This guide is designed to support the Biochemistry 205 and Biochemistry 420 assignments to research and write an essay on a selected protein. The first section is arranged in the order that one might work through the research process. However, you may also go to any of the sections in the alphabetical grouping above. Print material required for researching proteins is located in ISEL (Integrated Sciences & Engineering Library).
Where Do I Begin?
Selecting a Protein. Browsing articles in current and past issues of the journals listed in Journals, Periodicals may provide ideas. Or go to the European Bioinformatics Institute's InterPro:Protein of the Month for recent noteworthies with good overviews.
Properties. The Merck Index (UM Sci Ref
RS51 .M4 2001)
and The Dictionary of Organic Compounds (DOC) (UM Sci Ref QD246 .D52 1996 +) should be early stops as they include extensive information, and may determine whether your chosen protein meets the parameters of the assignment. Other Reference Materials should also be checked. Make note of the CAS registry number of your protein to simplify researching your protein in SciFinder Scholar. There are also two databases listed in Internet Resources that will help with molecular weight.
Occurence. The UniProt Knowledgebase reveals a broad picture of species occurence of a given protein. Following the associated links will also provide additional information and references relevant to parts of the assignment.
History. Reference Materials may provide basic information. You will also need to search for Books and journal articles in Databases.
Books Search for books in the Library Catalog. You may search for your specific protein, or even by type, i.e. enzymes, hormones, etc. To perform a subject search fromthe Basic Search page, choose "Subject keywords" from the menu on the left.
Sample subject searches:
Actin
Albumins
Blood Proteins
Carrier Proteins
Enzymes
Glycoproteins
Histones
Microbial Enzymes
Proteins structure
Somatotropin
You may also search the Virtual Catalog for holdings in other academic libraries in New England and public libraries in Massachusetts. You can then generate a loan request for available items. If you have identified a title not found in Library Catalog, you may request that the Library obtain it through Interlibrary Loan.
Databases Locate citations, abstracts and/or full text of journal articles, dissertations, government documents, and other information sources on your subject.
Please note: In some of our databases you may see the UMLinks button - . Clicking on this button will take you directly to the full text of your article, if available, or to other options for finding the article if not available online. For more information, see Frequently Asked Questions about UMLinks.
Biological Abstracts - Citations and abstracts for journal articles, conference papers, and books relating to life sciences. 1980-
CAB Abstracts - Useful for agricultural or food-related proteins. 1973-
PubMed - Comprehensive source of journal citations for medical and health-related information. 1966-
Suggestions for getting more out of PubMed:
MeSH (Medical Subject Heading). In the drop-down menu of the Search box select MeSH, and enter your protein name in the next box. Results will identify relevant terminology and definitions. There may be more than one result. Pick the best one, which will lead to a page of subheadings and a hierarchy of terms in which your protein falls. Check one of the subheadings, e.g. history or chemistry. Scroll up the page to Send to Search Box. Then choose Search PubMed. Hopefully, you have now reduced thousands of citations to a more manageable and appropriate number.
Proteins. You may also select Proteins in the drop-down menu. Resulting references are to articles specifically about protein sequences.
Entrez, The Life Sciences Search Engine. Convenient cross-database search page lists all NLM-related databases, i.e. protein sequence, 3D structure, books, and permits simultaneous or individual searching of them.
SciFinder Scholar - Chemical Abstracts Service (CAS) databases of chemistry and related scientific fields, particulary strong in bio-medicine. 1907-
Web of Science - Science Citation Index segment can be searched by topic, author, source, address or by cited reference for scholarly article citations. 1945-
WorldCat - Combined catalog of most U.S. libraries and some outside the U.S. leads to books, dissertations, and often to chapters within books.
Journals, Periodicals Specific to This Subject Area The Library offers many journals in digital format. For a listing, select E-Journals on the the library's main web page. Click on the Category tab, and select Life Sciences from the box on the left. From the box on the right, select the appropriate subcategory. The number in parentheses is the number of electronic journal titles containing information related to that subcategory. Once you click on the subcategory, a list of the e-journals will appear.
A selection of scholarly or academic journals follows:
Advances in Protein Chemistry (UM SciQD 431 .A3)
Journal of Biological Chemistry Online and in print (UM Sci Per QP 501 .J7)
ProteinsOnline and in print (UM Sci Per QP 551 .P69778)
Locating Materials within the Libraries After you have the citationfor your material (from a database, library catalog etc.) find the call number. If not available in the database or index you are using go to the Library Catalog.
Choose Title begins wth and type the name of the journal title, book or other material in the box that appears.
If your title appears write down the call number given and location (UM W.E.B. Du Bois, UM Science - Integrated Sciences & Engineering Library, Special Collections etc.).
Consult the Call Number chart to identify the floor for your material.
If this library doesn't own the material you want, try searching for an item from the Four College Catalog, or fill out an Interlibrary Loan Request Form with the appropriate citation information. Staff will attempt to locate and bring the material here for you to use.
Biochemistry. J.M. Berg et al. Searchable biochemistry text book.
ChemIDplus. National Library of Medicine. Provides substance name, synonyms, registry numbers, and sources of information.
Compute pI/Mw Tool. Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) with Swiss-Prot protein identifiers (ID) or Swiss-Prot/TrEMBL accession numbers (AC) found in UniProt Knowledgebase.
Molecules to Go. National Institutes of Health. Simple search provides text and various viewing options of graphic molecular structure. In the Output Requested drop-down menu, check the Stride option for secondary structure.
PDB Format. Eric Martz, University of Massachusetts. Key to Protein Data Bank files.
PDBsum. Roman Laskowski et al. University College London. Contains summary information and derived data on entries in the Protein Data Bank.
Protein Explorer. Eric Martz, University of Massachusetts. Award-winning site facilitates 3D visualization of proteins. Includes a useful glossary and other instructive suggestions. Spanish version available.
. Clicking on this button will take you directly to the full text of your article, if available, or to other options for finding the article if not available online. For more information, see Frequently Asked Questions about UMLinks.
