LOPAL and SCAMP: techniques for the comparison and display of protein structures |
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| Affiliation: | 1. iTHES Research Group and Theoretical Molecular Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan;2. Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;3. Faculty of Biology-Oriented Science and Technology, KINDAI University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan;4. Department of Molecular Sciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, United States;5. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States;6. Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States;7. Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan;1. State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, China;2. Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China;3. Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin 300457, China |
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| 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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