Principles of Protein Structure Assignment 1996
Index to Assignments
Instructions for Assignment 1
These instructions relate to the first formally assessed assignment, which
focusses on structural and sequence-related issues relating to the protein
insulin.
The following paragraphs outline some useful resources on the WWW that will
be of use.
Working through the assignment
The assignment has been designed to be worked through using RasMol. Several
(mostly short) RasMol scripts are included. However, it is not essential to
use RasMol- use a different molecular graphics package if you prefer.
The RasMol documentation, including Command Reference, is also on the WWW,
in the PPS2 hypertree, and
also at
Brookhaven National Laboratories Structural Biology Department.
Sequence Databases
The assignment involves retrieving some sequences from databases. A
recommended starting point is the OWL composite sequence database. If
necessary, refer to
the following description (part of Section 5 of the course) of composite
sequence databases (especially OWL):
OWL can be accessed from the UK and USA:
Two of the sources of OWL are the protein Sequence database SWISS-PROT at
ExPASy, and the gene sequence database GenBank, at the NCBI (the gene
sequences are translated to provide the protein sequences for OWL).
- they can of course be searched individually, as well as via OWL.
Submitting your answers
You may submit your answers in one of two ways: either 1) use the WWW form
provided or 2) simply e-mail them to
pps2@mail.cryst.bbk.ac.uk.
- Using the WWW form
- The assignment is split over 2 Web-pages, each with its own form (Questions
1-10 are covered by the first form and Question 11-17 by the second form).
These must therefore be submitted separately. Please include your name in the
box provided (on each page), and your e-mail address; also as an additional means of identification
please include the 4-character code of the PDB structure assigned to you,
again on each page.
IF YOU CHANGED YOUR PDB CODE AND HAVE NOT INFORMED THE COURSE ORGANIZERS,
PLEASE DO SO AS SOON AS POSSIBLE, BEFORE SUBMITTING THE ASSIGNMENT.
Note that although the assignment includes multiple questions, there will NOT
be an immediate automatic response informing you of which ones you answered
correctly.
AFTER YOU HAVE SUBMITTED THE ANSWERS TO ALL THE FORMS, PLEASE E-MAIL
pps2@mail.cryst.bbk.ac.uk
WITH THE SUBJECT HEADING "PPS ASSIGNMENT 1 COMPLETED" INCLUDING YOUR NAME
AND E-MAIL ADDRESS IN THE BODY OF THE MESSAGE.
- Using E-mail
- Edit this blank form to fill in the blanks:
Name, E-mail Address; also as an additional means of identification
please include the 4-character code of the PDB structure assigned to you.
For the multiple choice questions, simply indicate your answers by placing
an asterisk ('*') next to the appropriate letter (a,b,c or d).
PLEASE E-MAIL THIS FORM TO
pps2@mail.cryst.bbk.ac.uk
WITH THE SUBJECT HEADING "PPS ASSIGNMENT 1 COMPLETED" INCLUDING YOUR NAME
AND E-MAIL ADDRESS IN THE BODY OF THE MESSAGE. Your submission will be
acknowledged as soon as possible.
Index to Assignments
Last updated 11th Apr '96