A Library of Protein Family Cores

Russ Altman
Bob Schmidt
Mark Gerstein

We have taken structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures.

 The Library of Protein Family Cores

• Core Structure Sublibraries (all current computed cores, organized by multiple alignment method)
• Searching LPFC
• PDB Structure List (list of all PDB structures used in core calculations; not yet completed)

 Background

• Project Overview (personnel, miscellaneous shared data, references)
• Code and Documentation (Perl scripts, C code, and README file for core-finding)
• Related Links of Interest

1. Schmidt, R.B., Gerstein M., and Altman, R.B. LPFC: A Library of Protein Family Core Structures, Protein Science, 1997 Jan;6(1):246-8
2. Gerstein, M., and Altman, R.B., Using a measure of structural variation to define a core for the globins, Comput Appl Biosci 1995 Dec;11(6):633-44
3. Gerstein, M., and Altman, R.B., Average Core Structures and Variability Measures for Protein Families: Application to Immunoglobins,J. Mol. Biol. 251:161-175, 1995.
4. Altman, R.B. and Gerstein, M. Finding an average core structure: Application to the globins. Proceedings of Second International Conference on Intelligent Systems for Molecular Biology, Stanford, August 1994, AAAI Press, Menlo Park, p. 19-27.
5. Altman, R.B., Hughes, C, and Gerstein, M.B., Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins, J. Mol. Graphics, 13:142-152, 1995.

 

 
 
 
 
 

Acknowledgements
 

• We thank Vui Chiap Lam for his MVP2WRL converter program.