Studying Sequence-Structure Relationships with Annotated Alignments

Studying Sequence-Structure Relationships
with Annotated Alignments

This includes constructing templates for use in "threading" sequences onto structures, looking for correlated mutations at different positions in a protein sequence, and trying to understand how particular sequences give rise to specific structural features.

Some useful links to alignments and classifications of proteins

The Dali server and FSSP database at EMBL
The California version of SCOP
CATH in London
Barton group server at Oxford
ABS classification at NIH

Library of Average Protein Core Structures

Annotated Alignments of specific families

Immunoglobulins
- VL-VH average core
- picture (VH)
Globins
- Coordinates of an average core
- sequence alignment (577 sequences)
- picture
Dihydrofolate-Reductase
- sequence alignment
Plastocyanin-Azurin
- sequence alignment

My .emacs file

This includes elisp code to color and edit a multiple alignment.

Papers

M Gerstein, E Sonnhammer & C Chothia (1994). "Volume Changes on Protein Evolution," J. Mol. Biol. 236: 1067-1078.
- [Medline Abstract for 94166074] [ftp directory with text + programs + alignments]
M Gerstein & R Altman (1995). "Average core structures and variability measures for protein families: Application to the immunoglobulins," J. Mol. Biol. 251: 161-175.
- [ftp directory with text + other stuff]
M Suzuki & M Gerstein (1995). "The geometry of alpha-helices binding to DNA," Proteins: Struc. Func. Genet. 23: 525-535.
M Gerstein & M Levitt (1996). "Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures," in Proceedings of the Fourth International Conferene on Intelligent Systems in Molecular Biology, (Menlo Park, CA, AAAI Press, June 12-15), 59-67.
- [manuscript text in available in a variety of formats]

10 November 1995 / mark.gerstein@yale.edu