LOPAL and SCAMP: techniques for the comparison and display of protein structures

Geoffrey J. Barton (Lead / Corresponding author), Michael J.E. Sternberg

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)

Abstract

This paper describes two computer programs designed to assist in the comparison of protein structures. LOPAL (LOoP ALignment) applies a dynamic programming algorithm to the comparison of regions of protein three-dimensional (3D) structure and gives a similarity score and suggested sequence alignment with that score. SCAMP (Structure Comparison and Alignment of Multiple Proteins) is an interactive graphics program for the Evans and Sutherland PS300 graphics terminal that allows the simultaneous display, manipulation and pairwise least-squares fitting of up to nine independent structures. Together, LOPAL and SCAMP provide an integrated system for characterizing structural similarities in proteins with the aim of improving the accuracy of predicted protein structures. An application of these programs to loop regions in the immunoglobulin constant domains is illustrated.

Original languageEnglish
Pages (from-to)190-196
Number of pages7
JournalJournal of Molecular Graphics
Volume6
Issue number4
DOIs
Publication statusPublished - Dec 1988

Keywords

  • automatic structure comparison
  • dynamic programming
  • immunoglobulin
  • least-squares fitting
  • protein structure
  • PS300 graphics program

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