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Other non-free, shareware programs include ICM-Browser, [23] MDL Chime, UCSF Chimera, Swiss-PDB Viewer, [24] StarBiochem [25] (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius, and VisProt3DS [26] (a tool for Protein Visualization in 3D stereoscopic view in anaglyph and other modes), and Discovery ...
The RCSB PDB presently acts as the "archive keeper". This ensures that there is only one version of the data which is identical for all users. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public.
Protein Data Bank: Protein DataBank in Europe (PDBe), [18] ProteinDatabank in Japan (PDBj), [19] Research Collaboratory for Structural Bioinformatics (RCSB) [20] (PDB) Protein structure databases Structural Classification of Proteins (SCOP) Protein structure databases CATH database: Protein structure databases ModBase: Sali Lab, UCSF
SA Tableau Search Fast and accurate protein substructure searching with simulated annealing and GPUs: SSE: Pair: No: download server: A.Stivala et al. 2010 RCSB PDB Protein Comparison Tool Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments: Cα: Pair: yes: server download: A. Prlic et al. 2010 CSR
Chime was used by a wide range of biochemistry web sites for the visualization of macromolecules, many of which were linked to the World Index of Molecular Visualization Resources MolVisIndex.Org. Chime was also used until 2006 at the Protein Data Bank (PDB) to examine structures stored there.
Protein Data Bank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography , protein NMR spectroscopy, or cryogenic electron microscopy .
"OrgSyn search". PDB PDBe Protein Data Bank in Europe EMBL-EBI: has some chemicals as well as proteins "PDBe". PATENTSCOPE: WIPO "PATENTSCOPE". 16,000,000 PDB RSCB Protein Data Bank "PDB". 166,891 PharmGKB Shriram Center for Bioengineering and Chemical Engineering drugs targets prescribing info curated "PharmGKB". PHAROS Illuminating the ...
PDB Format Guide This is the current version (3.3) of the PDB format specification. PDBML A more recent, alternative XML-based file format for molecular coordinates. The RCSB Protein Data Bank; Protein Data Bank in Europe; The Molecular Modeling DataBase (MMDB) from NCBI; The wwPDB remediation Project from wwPDB