蛋白质生物信息学-数据库.ppt

Protein 结构数据库 汪德强 Ph. D 医学检验系 感染性疾病分子生物学重点实验室 E-mail: cquwangdq@163.com Protein Data Bank The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. New structures are released each Wednesday by 1:00am Pacific time. The contents are primarily experimental data derived from X-ray crystallography and NMR experiments. RCSB PDB Members The PDB is managed by three participating sites of the Research Collaboratory for Structural Bioinformatics (RCSB) consortium:1,Rutgers, the State Universityof New Jersey2,San Diego SupercomputerCenter (SDSC)3,Center for Advanced Research in Biotechnology (CARB) What information dose PDB contain A variety of information associated with each structure is available, including sequence details, atomic coordinates, crystallization conditions, 3-D structure neighbors computed using various methods, derived geometric data, structure factors, 3-D images, and a variety of links to other resources. Folds? What Data Formats are Supported STRUCTURE FILE 1. The PDB format widely accepted by the community and all software that uses structure information uses this format by default. All new PDB files being produced conform to v2.2 of the PDB format. File names are of the form pdbxxxx.ent where xxxx is the PDB ID. The mmCIF format macromolecular Crystallographic Information File 3. The XML format PDB File Format Preface The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. PDB File Format Text – you can edit with Pico, Notepad… Rich annotation Format described in PDB File Format Contents Guide Version 2.2 (20 De