PAST: Fast Structure-based Searching in the PDB

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jul 18

PMID 16844992

Citations 10

Authors

Hanjo Taubig

Arno Buchner

Jan Griebsch

Affiliations

Soon will be listed here.

Abstract

PAST is a new web service providing fast structural queries of the Protein Data Bank. The search engine is based on an adaptation of the generalized suffix tree and relies on a translation- and rotation-invariant representation of the protein backbone. The search procedure is completely independent of the amino acid sequence of the polypeptide chains. The web service works best with, but is not necessarily limited to, shorter fragments such as functional motifs-a task that most other tools do not perform well. Usual query times are in the order of seconds, allowing a truly interactive use. Unlike most established tools, PAST does not prefilter the dataset or exclude parts of the search space based on statistical reasoning. The server is freely available at http://past.in.tum.de/.

Citing Articles

Protein Function Prediction Based on PPI Networks: Network Reconstruction vs Edge Enrichment.

Zhou J, Xiong W, Wang Y, Guan J Front Genet. 2021; 12:758131.

PMID: 34970299 PMC: 8712557. DOI: 10.3389/fgene.2021.758131.

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.

Sehnal D, Pravda L, Varekova R, Ionescu C, Koca J Nucleic Acids Res. 2015; 43(W1):W383-8.

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INTEGRATING COMPUTATIONAL PROTEIN FUNCTION PREDICTION INTO DRUG DISCOVERY INITIATIVES.

Grant M Drug Dev Res. 2014; 72(1):4-16.

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Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks.

Xiong W, Liu H, Guan J, Zhou S BMC Bioinformatics. 2013; 14 Suppl 12:S4.

PMID: 24267980 PMC: 3848795. DOI: 10.1186/1471-2105-14-S12-S4.

Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

Malhotra S, Sowdhamini R BMC Bioinformatics. 2012; 13:165.

PMID: 22800292 PMC: 3472317. DOI: 10.1186/1471-2105-13-165.

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