Tag: PDBE

EMDB < EMD-20433

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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metY SAM V (53-MER) from Candidatus Pelagibacter ubique HTCC1062 (PDB 6FZ0, chain A)

Javascript is currently disabled or is not supported by this browser. Please enable JavaScript for full functionality. Sorry, there was a problem loading sequence from server. Please try again and contact us if the problem persists. Automated summary: This ncRNA sequence is 53 nucleotides long and is found in Candidatus…

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Empathy List Archives

Dear colleagues, Data on sequence level mapping through the SIFTS process www.ebi.ac.uk/pdbe/docs/sifts/ can now be retrieved directly from updated mmCIF files, available on PDBe entry pages. These files now contain residue-level mapping between UniProt and PDB entries, including coordinate numbering for UniProt accessions and mapping to a host of other…

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[ccp4bb] Vacancy for EMDB Team Leader (EMBL Faculty position)

Dear colleagues, EMBL-EBI is looking to recruit a new Team Leader (EMBL Faculty position) to take charge of the Electron Microscopy Data Bank (EMDB; emdb-empiar.org), one of the three core archives of the Worldwide Protein Data Bank organisation (wwPDB; wwpdb.org). In the past two years, EMDB has doubled in size…

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Predicted complexes from ModelArchive now on PDBe-KB pages

High-quality, predicted protein complexes, generated using RoseTTAFold and AlphaFold, are now available in ModelArchive and accessible through the 3D-Beacons Network. These predicted complexes are also integrated into the PDBe-KB aggregated views of proteins. High-quality, predicted protein complexes, generated using RoseTTAFold and AlphaFold, are now available in ModelArchive and accessible through…

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[PyMOL] PyMol & PDBe

Hi Filip, This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it’s backwards compatible. The only difference is the file format, previously we downloaded omap format, now it’s ccp4 map format (larger files but higher…

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Bioinformatician/Scientific Programmer job with EMBL

We seek to recruit a structural bioinformatician who is interested in working on the intersection of bioinformatics and cheminformatics. The post holder will join the Velankar team at EMBL-EBI on a 2-year collaborative project between PDBe, ChEMBL and CCDC. They will contribute to improving data processing pipelines to increase the…

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Local Biocuration Conference

About PDBe > Upcoming Events > Local Biocuration Conference Local Biocuration Conference Event details Event Date: Thursday, May 5, 2022 to Friday, May 6, 2022 People: Simone Weyand (delegate) Location: Wellcome Genome Campus Hinxton The event will be two full days and the programme highlights include: Two Keynote lectures covering…

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Bioinformatician job with EMBL | 1401746299

Are you creative, curious, and ambitious and like to tackle challenging biological data analysis problems? We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). In this…

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A guide to analysing binding sites in protein structures

This webinar gives an introduction to the information required to effectively interpret ligand binding sites in protein structures. It will highlight tools available at the Protein Data Bank in Europe (PDBe) and PDBe Knowledge Base (PDBe-KB) to analyse ligand binding pockets and interactions. It will also highlight how this information…

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Beauty at a molecular level

About PDBe > News > 2022 Calendar: Beauty at a molecular level 2022 Calendar: Beauty at a molecular level ‘Tis the season for the new PDBe calendar! Our calendar for 2022 is now available to view and print – just in time for the New Year. The PDBe calendar for 2022 is…

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PDBe Download Service for bulk download of data

The PDBe pages provide a number of tools and visualisations to support analysis and understanding of PDB structures, however sometimes it is still necessary for users to have access to the data files. We have now introduced a file download service, allowing users to easily download coordinates and related data…

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Bioinformatician – Hinxton | Mendeley Careers

We are looking for a structural bioinformatician who is interested in developing methods for protein structure analysis to identify biologically relevant conformational states and link these to macromolecular function. The post holder will join the Velankar team at EMBL-EBI on a 3-year collaborative project between Protein Data Bank in Europe…

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PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe – Knowledge Base (PDBe-KB, pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by…

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Faster way to download PDBe PISA data

Faster way to download PDBe PISA data 1 I’m downloading PDBe PISA data as advised on the download page, via successive calls with lists of PDB codes such as www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?1kq1,4foj,3ga7,4err etc. The download time seems to be varying (in the last few sets of 50 interfaces it’s been between 3…

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how to download interface generated with PDBe PISA?

how to download interface generated with PDBe PISA? 1 I have a list of monomers, only one chain in the asymmetric unit of PBD entry. I want to generate crystal interface for these monomers using PISA server. I can do it online and download manually the interface with the larget…

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[ccp4bb] Bioinformatician position at PDBe

Dear Colleagues, We have an exciting opportunity for a bioinformatician interested in structural biological data and functional annotations to work within the Protein Data Bank in Europe Team (PDBe) at the European Bioinformatics Institute (EMBL-EBI). The work includes standardising post translational modification information within the PDB archive in collaboration with…

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See how students fused art and science for stunning 2021 PDB Art project

They are the building blocks of life – and their extraordinary structures have inspired these striking artworks from students in Cambridge and beyond. Each year, art students are invited to create pieces based on the Protein Data Bank in Europe (PDBe) – and this year’s work has gone on display…

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Stunning artworks from Cambridge school students inspired by Protein Data Bank to be exhibited

An exhibition of stunning artwork by students inspired by structures in the Protein Data Bank in Europe (PDBe) will be launched today (Friday, October 1). Hundreds of pupils from schools including The Perse and The Leys in Cambridge, Saffron Walden County High and Thomas Gainsborough in Sudbury created pieces for…

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3D-Beacons Network: protein structure data, all in one place

3D-Beacons Network acts as a one-stop shop for protein structures by combining and standardising data from several providers Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome. Image obtained from PDBe A new platform called 3D-Beacons Network brings together experimentally determined and predicted protein structure models and related…

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Apply for AlphaFold DB Full-Stack Web Developer in Essex

We are looking for a full-stack web developer interested in structural biological data and predicted structures in the AlphaFold Protein Structure Database (AlphaFold DB) to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI). This is an exciting opportunity to work as part of EMBL and DeepMind’s new partnership…

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Ligand GNP bound in PDB entry 7obq ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

  The above 2D and 3D (Mol*) views of ligand interactions use quaternary structure derived from the PDB entry. Please note: Some chain IDs in the tooltip are followed by a number in square brackets. This number corresponds to the operation ID (mmCIF ‘oper_expression’) used to transform the chain. The…

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how to find interference residue

how to find interference residue 1 Are you asking about interacting residue in protein-protein interfaces? If so, this server takes a PDB file and will calculate the interface residues. www.ebi.ac.uk/pdbe/pisa/ Login before adding your answer. Traffic: 1660 users visited in the last hour Read more here: Source link

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