Search the Web
- This is another way to search the literature Google Scholar
- Wikipedia I go here first – use it as an in-depth dictionary
- PubMed: Free everywhere from N.I.H. very good and fast (their help pages).
- Don’t forget YouTube There is actually a lot of good science – nice animations.
- How to read scientific papers – while this says it is for non-scientists it’s actually very good. You should read several papers at this level for this class. One trick will be looking through many papers to decide which few you will work through. But that’s one of the things you will get to practice here.
Now that you have found a reference can you get the paper? Often Yes! - Often PubMed will bring you to a link for a free copy of the paper.
- Free from a CUNY (or CITY) I.P. address
- American Chemical Society– Many important journals.
– Even more important journals
Web of Science Especially good to find papers that cite a paper you like.
Library:
- CCNY library connections to journals and search engines that are free from a CUNY I.P. address; More than what is available from CUNY (look at Online Electronic Journals). how to use a proxy account from home, interlibrary loans.
Biophysics resources on the web
- Protein data bank: use this to get data files and other useful information about proteins
- pdb documentation links
- good description of amino acids |
A protein structure class website from Birkbeck College
Visualizing proteins on your computer:
- Chimera from the Resource for Biocomputing, visualization and informatics
- PYMOL Open source, flexible. manual
VMD From the Schulten lab a U of Ill. - Rasmol A molecule viewer that will run on any computer. Good tutorial.
- Swiss PDB viewer More sophisticated than RASMOL but its also ok.
If you don’t have Word/Powerpoint/Excel you can get OPEN OFFICE for free.
Databases:
SCOP A listing of all pdb files sorted by structure (my favorite)
membrane proteins of known structure (from Steve White)
Textbooks online:
- Pub med has several text books online
a nice biochemistry web site
FOLDIT at home – A computer game that lets you fold proteins
