EurekaMag
+ Translate
+ Most Popular
The pigeon tick (Argas reflexus): its biology, ecology, and epidemiological aspects
Prevalence of hemoglobin abnormalities in Kebili (Tunisian South)
Lipogranuloma: a preventable complication of dacryocystorhinostomy
Value of basal plasma cortisol assays in the assessment of pituitary-adrenal insufficiency
Bees from the Belgian Congo. The acraensis group of Anthophora
Placing gingival retraction cord
Total serum IgE, allergy skin testing, and the radioallergosorbent test for the diagnosis of allergy in asthmatic children
Acariens plumicoles Analgesoidea parasites des oiseaux du Maroc
Injuries of terminal phalanges of the fingers in children
Biology of flowering and nectar production in pear (Pyrus communis)
Das Reliktvorkommen der Aspisviper (Vipera aspis L.) im Schwarzwald
Hydrological modelling of drained blanket peatland
Pathologic morphology and clinical significance of the anomalous origin of the left circumflex coronary artery from the right coronary artery. General review and autopsy analysis of 30 cases
Cyto genetic analyses of lymphocyte cultures after exposure to calcium cyclamate
Axelrodia riesei, a new characoid fish from Upper Rio Meta in Colombia With remarks concerning the genus Axelrodia and description of a similar, sympatric, Hyphessobrycon-species
Favorable evolution of a case of tuberculosis of pancreas under antibiotic action
RIFM fragrance ingredient safety assessment, Valencene, CAS Registry Number 4630-07-3
Parenteral microemulsions: an overview
Temperate pasture: management for grazing and conservation
Evaluation of a new coprocessed compound based on lactose and maize starch for tablet formulation
Thermal expansion and cracking of three confined water-saturated igneous rocks to 800C
Revision of the genera of the tribe Stigmoderini (Coleoptera: Buprestidae) a discussion of phylogenetic relationships
Anal tuberculosis. Report of a case
Gastric tuberculosis in the past and present
Adaptive responses of the cardiovascular system to prolonged spaceflight conditions: assessment with Holter monitoring

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer


Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer



Computer Applications in the Biosciences: Cabios 11(6): 675-679



ISSN/ISBN: 0266-7061

PMID: 8808584

DOI: 10.1093/bioinformatics/11.6.675

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the O-C-C-O pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acidresidues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 009299116

Download citation: RISBibTeXText

Related references

Three-dimensional structure of protein C inhibitor predicted from structure of alpha 1-antitrypsin with computer graphics. Protein Engineering 1(6): 471-475, 1987

Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. Journal of Molecular Biology 232(3): 805-825, 1993

Three-dimensional profiles for analysing protein sequence-structure relationships. Faraday Discussions 1992(93): 25-34, 1992

Automatic classification of protein sequences into structure/function groups via parallel cascade identification: A feasibility study. Annals of Biomedical Engineering 28(7): 803-811, 2000

Three-dimensional structure of CA1 pyramidal cells in rat hippocampus--optical recording of LSM and computer simulation of fractal structure. Science in China. Series B Chemistry Life Sciences and Earth Sciences 38(10): 1187-1194, 1995

Three-dimensional shape-structure comparison method for protein classification. Ieee/Acm Transactions on Computational Biology and Bioinformatics 3(3): 193-207, 2006

Use of restrained molecular dynamics in water to determine three-dimensional protein structure: prediction of the three-dimensional structure of Ecballium elaterium trypsin inhibitor II. Proteins 6(4): 405-417, 1989

Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure. Nucleic Acids Research 14(1): 381-387, 1986

Three-dimensional structure for the b2 adrenergic receptor protein based on computer modeling studies. Journal of Molecular Biology 225: 9-71, 1992

Automatic classification of protein structures using low-dimensional structure space mappings. Bmc Bioinformatics 15 Suppl. 2: S1, 2014

Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel beta roll motif. Embo Journal 12(9): 3357-3364, 1993

Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies. Journal of Molecular Biology 225(3): 859-871, 1992

Analysis of protein patterns during differentiation using 2 dimensional electrophoresis and computer multi dimensional classification. Electrophoresis 4(1): 63-70, 1983

Protein structure comparison using bipartite graph matching and its application to protein structure classification. Molecular and Cellular Proteomics: Mcp 1(4): 334-339, 2002

Three-dimensional structure of the metastasis-promoting protein MIA The first extracellular protein adopting a SH3 domain-like structure. Journal of Cancer Research and Clinical Oncology 127(Suppl. 1): S65, 2001