{"doi":"10.1093/bioinformatics/btq572","title":"Pre-calculated protein structure alignments at the RCSB PDB website","abstract":"<h4>Summary</h4>With the continuous growth of the RCSB Protein Data Bank (PDB), providing an up-to-date systematic structure comparison of all protein structures poses an ever growing challenge. Here, we present a comparison tool for calculating both 1D protein sequence and 3D protein structure alignments. This tool supports various applications at the RCSB PDB website. First, a structure alignment web service calculates pairwise alignments. Second, a stand-alone application runs alignments locally and visualizes the results. Third, pre-calculated 3D structure comparisons for the whole PDB are provided and updated on a weekly basis. These three applications allow users to discover novel relationships between proteins available either at the RCSB PDB or provided by the user.<h4>Availability and implementation</h4>A web user interface is available at http://www.rcsb.org/pdb/workbench/workbench.do. The source code is available under the LGPL license from http://www.biojava.org. A source bundle, prepared for local execution, is available from http://source.rcsb.org<h4>Contact</h4>andreas@sdsc.edu; pbourne@ucsd.edu.","journal":"Bioinformatics","year":2010,"id":4715,"datarank":0.7947476049822055,"base_score":5.298317366548036,"endowment":5.298317366548036,"self_citation_contribution":0.7947476049822055,"citation_network_contribution":0.0,"self_endowment_contribution":0.7947476049822055,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":199,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0724,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2010-10-10","fair_score":67.5,"fair_percentile":95.7,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":5440,"name":"Spencer E. 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