2004
DOI: 10.1093/nar/gkh436
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ProteinDBS: a real-time retrieval system for protein structure comparison

Abstract: We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time. This system applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. When meaningful contents, represented in a multi-dimensional feature space, have been extracted from distance matrices, an advanced indexing structure, Entropy Balanc… Show more

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Cited by 29 publications
(21 citation statements)
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“…ProteinDBS uses computer vision techniques to align two protein chains based on the two-dimensional distance matrix generated from the 3D coordinates of the alpha-carbon atoms on the protein backbones. The two chains 1o7j.a and 1hfj.c are examples given in the ProteinDBS paper 16 . According to the query result from the ProteinDBS website, the seven chains (1hfj.c, 1qd1.b, 1toh, 4eca.c, 1d9q.d, 4eca.b, 4eca.d) have global tertiary structures most similar to 1o7j.a.…”
Section: The Experimentsmentioning
confidence: 99%
“…ProteinDBS uses computer vision techniques to align two protein chains based on the two-dimensional distance matrix generated from the 3D coordinates of the alpha-carbon atoms on the protein backbones. The two chains 1o7j.a and 1hfj.c are examples given in the ProteinDBS paper 16 . According to the query result from the ProteinDBS website, the seven chains (1hfj.c, 1qd1.b, 1toh, 4eca.c, 1d9q.d, 4eca.b, 4eca.d) have global tertiary structures most similar to 1o7j.a.…”
Section: The Experimentsmentioning
confidence: 99%
“…Another comparison technique based on computer vision algorithm was published by Shyu an co-workers [82] and was made available as a web-based server that allows one to retrieve information from the Protein Data Bank or from e SCOP database. The technique was validated against several hundreds of SCOP entries and shows a precision of 84% at the 10% recall rate, and of 49% at the 100% recall rate.…”
Section: Proteindbsmentioning
confidence: 99%
“…A much faster search engine for protein structure comparison, ProteinDBS [121], was developed recently. Based on the alignment between the query protein structure and the hits in the structure database, one may find biologically interesting similarities that are not detectable by sequence comparison or threading.…”
Section: Structure-structure Comparisonmentioning
confidence: 99%