Studying Sequence-Structure Relationships
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.
with Annotated Alignments
Some useful links to alignments and classifications of proteins
Annotated Alignments of specific families
- This includes
elisp code to color and edit a multiple alignment.
10 November 1995 /
- M Gerstein, E Sonnhammer & C Chothia (1994). "Volume Changes on
Protein Evolution," J. Mol. Biol. 236: 1067-1078.
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:
- 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]