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Zinc is one of the most important biologically active metals. Ten per cent of the human genome is thought to encode a zinc binding protein and its uses encompass catalysis, structural stability, gene expression and immunity. At present, there is no specific resource devoted to identifying and presenting all currently known zinc binding sites. Here we present ZincBind, a database of zinc binding sites and its web front-end. Using the structural data in the Protein Data Bank, ZincBind identifies every instance of zinc binding to a protein, identifies its binding site and clusters sites based on 90% sequence identity. There are currently 24 992 binding sites, clustered into 7489 unique sites. The data are available over the web where they can be browsed and downloaded, and via a REST API. ZincBind is regularly updated and will continue to be updated with new data and features.
Pubmed ID: 30722040
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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute).
View all literature mentionsDjango is a high-level Python Web framework that encourages rapid development and clean, pragmatic design. Developed four years ago by a fast-moving online-news operation, Django was designed to handle two challenges: the intensive deadlines of a newsroom and the stringent requirements of the experienced Web developers who wrote it. It lets you build high-performing, elegant Web applications quickly. Django focuses on automating as much as possible and adhering to the DRY principle.
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