... stops working on a system where it used to work before.1 Please read Using PDBj's web interface and confirm whether your ... your graphics driver to the latest version. 1) This issue has been reported on Windows 8.1 + Firefox 43.0.4 + NVIDIA driver ...

... of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 1, 2020 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots ... archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 1, 2020 can be found in ftp://ftp.ebi.ac.uk/pub/databases ...

... file is required to deposit NMR structures after February 1, 2008. (version 1) There is no restriction on the format for the ... 2 NMR restraints files are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom ...

... above a certain threshold (Sequence identity30% and E-value0.1) arelinked. The set is first clustered using single-linkage ... these clusters are partitioned by the following iterative procedure: 1. The structure with the greatest number of links is chosen ...

... from Bacillus cereus that was co-crystallized with zinc and acetate[1]. [Usage] Here we will demonstrate how Structure Navigator can ... site based on the position of the conserved loop? [References] 1. Handa N, Terada T, Kamewari Y, Hamana H, Tame JR ...

... stabilise the C-terminal region of human glutathione transferase A1-1: a crystallographic and calorimetric study (2005) J.Mol.Biol ... large, diverse and demanding global community of users. (1) Announcing the worldwide Protein Data Bank. Berman H, Henrick ...

... (https://files.wwpdb.org/, https://s3.rcsb.org) as of January 1, 2025 has been added to https://s3snapshots.rcsb.org/, snapshots.rcsb.org ... the file was modified. The snapshot of PDB Core Archive is 1,437 GB. A snapshot of the EMDB Core archive (ftp://ftp ...

... and processes for maintaining and extending the data standard [1]. Visit the ModelCIF GitHub for more information about this ... data information framework. [1] Vallat B, Tauriello G, Bienert S, Haas J, ...

... pertaining to these data. These extensions cover three main areas: 1. scaled and merged reflection data that have been processed to ... , by providing descriptors for that anisotropy, in terms of (1) a parameter-free definition of a cut-off surface by ...

... Data Bank Japan (PDBj, head Prof. Genji Kurisu)*1, operated by the Institute for Protein Research at Osaka University ... Institute for Protein Research, the University of Osaka Terminology *1 Protein Data Bank Japan :PDBj head Prof. Genji Kurisu ...

... the latest version. Java applet in the web site (*1) Updating is necessary when it refers the jV software placed ... launching the jV will fail because the certificate expired. *1: Currently, some latest web browsers such as Firefox and Google ...

... There are two ways to provide your query structure, by either 1. specifying a PDB ID, or 2. uploading a PDB- ... the alignment page to see the actual superposition. [References] 1. Similarity search for local protein structures at atomic resolution by ...

... , you can use the PDBj Mine. The procedure is described below. 1. At the top of the page you can find a search field ... which is involved in your interest keywords. The procedure is described below. 1. At the top of the page you can find a search field ...

... NMR restraints file is mandatory for NMR structures deposited after February 1, 2008. For more details, please see the main page ... is mandatory for X-ray diffraction structures deposited after February 1, 2008. For more details, please see the main page ...

What is SIFTS? SIFTS*1 (Structure integration with function, taxonomy and sequence) is an up-to-date ... [] -- The same as above but in an array of text (for convenience). ); *1) Velankar et al., Nucleic Acids Research 41, D483 (2013)

... , respectively, and over two million atoms each. The HIV-1 capsid is the protein envelope that encloses and protects the RNA ... /EMD-5639/map/emd_5639.map.gz Reference Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular ...

jV 4.5.1." /> PDBj announces the bug fix update of the molecular viewer jV 4.5.1. The difference from the previous version (4.5) is that the bug fix involved in writing static image into directories without permission.

... for any part of PDB IDs like the following examples. e.g.1) PDB IDs start with1A 1A* e.g.2) PDB IDs end ... a month only. e.g.) search for January, 2008 OK: after January/1/2008 before January/31/2008 NG: after January/ (blank) /2008 before January ...

... . nouveau), please try to install an alternative graphics driver (e.g. NVIDIA).1 1) This issue has been reported on CentOS 6.7 + Firefox ESR 38 ...

... the deposition of chemical shift data in NMR-STAR (V3.1) format and perform checks to confirm the correspondence between the ... http://bmrb.pdbj.org/formats.html NMR-STAR 3.1 Dictionary Documentation http://bmrb.pdbj.org/dictionary/3.1html/SuperGroupPage. ...

... secondary structure assignment by W. Kabsch and C. Sander [1], you need to download the executable file for either Windows ... uses the information on secondary structure assignment in the PDB data. [1] W. Kabsch and C. Sander, Dictionary of protein secondary ...

... The information comes from several databases and literature sources. 1) Functional Information from GO Data The GO (GeneOntology) ... the catalytic residues from homologous enzymes is as follows: 1. Extract the PDB sequence from the original CATRES file ...

... 3.20 Changes Guide (PDF) highlights the changes in format from 3.1. Please send any questions to info@wwpdb.org.

... the center of the calculated map. The contour level is chosen as 1 sigma of the map for 2Fo-Fc and 2 sigma for Fo ...

... April 2019 (JST). Thank you for using this service so long. References 1. Similarity search for local protein structures at atomic resolution by exploiting a ...