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

Geoffrey J. Barton; Michael J.E. Sternberg

doi:10.1016/S0263-7855(98)80002-7

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

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

Computational Biology

Research output: Contribution to journal › Article › peer-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 language	English
Pages (from-to)	190-196
Number of pages	7
Journal	Journal of Molecular Graphics
Volume	6
Issue number	4
DOIs	https://doi.org/10.1016/S0263-7855(98)80002-7
Publication status	Published - Dec 1988

Keywords

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

ASJC Scopus subject areas

Biophysics
Biochemistry

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10.1016/S0263-7855(98)80002-7

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title = "LOPAL and SCAMP: techniques for the comparison and display of protein structures",

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.",

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AU - Sternberg, Michael J.E.

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N2 - 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.

AB - 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.

KW - automatic structure comparison

KW - dynamic programming

KW - immunoglobulin

KW - least-squares fitting

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

Abstract

Keywords

ASJC Scopus subject areas

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