Assignment 2

The Biological Internet

Finding your way about the Biological Internet is absolutely essential for modern biology and for this course! So here are some suggested tasks. They aren't as detailed as the first assigment.

Don't worry about WHAT you find when to get to a location, unless, of course you're interested :-) Just practice:

(a) finding the sites
(b) remembering them (use your hotlist)
(c) following links from one site to another.

There are several sites which contain pointers to other sites and are kept very much up-to-date by committed volunteers. try to find:

- the Virtual Library (at CERN)
- the Biology section of the Virtual Library
- the crystallography section of the VL

Often a good way to start is to go to a good home page (e.g. the Birkbeck Crystallography Home page) which will have links to many of the sites you want. Even if they aren't ALL there, when you go to other sites, THEY will have further pointers. If you are a specialist in one of the following, try to find pointers to:

- a virology resource
- a 7-transmembrane resource
- a globin resource
- or others of interest

(HINT - I think they can be found from the Biology VL in one or two hops).

Sites for Proteins

You will need to use the following resources a lot, starting in assignment 3 (if not before!):

- Protein Databank at Brookhaven
- SWISSPROT at Geneva
- Other ExPAsY services at Geneva
- GDB and services there

The main databases that you will need to know your way around are:

PDB
SWISSPROT
EMBL or GENBANK
SWISS3DIMAGE
EC (for enzymes)
GDB (for genomics - not essential)
OMIM (for diseases - not essential)

There are a number of sites which collate and interpret protein data.

Amongst these are:

SCOP (Cambridge)
SRS (Heidelberg - very impressive - but a learning curve)
Molecules 'R Us
Protein Motions

National and International Sites

Many countries have a national 'node' or centre for bioinformatics. In Europe we have EMBNET which has centres in all of its members. In the USA there are a number of Federally funded sites (not necessarily solely biological - e.g. Brookhaven). Find out whether your country has a site and a home page on it. Be careful not to bother them unnecessarily - don't ask them questions which the course is set up to do - but there may be useful discussions you could have about mirroring databases in your country.

Search Services

It is extremely useful to be able to search the WEB for information. There are a wide range of tools and indexes. Find one you are comfortable with. (I use Lycos - but there are several others). Learn how to phrase a question (so as to get a good signal to noise ratio).

As a brilliant way to start is the page of Hotlinks to protein-structure related databases put together for you by Ethan Benatan and Cornelius Krasel.

pmr 3rd.Feb'95

To Main PPS Index