Tag: PDBE

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

In an effort to improve the understanding of the structure and function of macromolecular assemblies, a new feature has been introduced to annotate and display symmetry in these structures. This new process, powered by Ananas, provides global symmetry data for each new assembly on a weekly basis. This underlying data…

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF…

The Protein Data Bank (PDB) [1], managed by the worldwide PDB (wwPDB) consortium [2], serves as the single global repository for information on 3D structures of proteins, nucleic acids, and complex assemblies. With over 200,000 entries as of July 2023, about 75% of these structures contain at least one small…

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

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…

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…

Large language models are changing the way we carry out scientific data curation, annotation, and research, setting the stage for a more efficient understanding of scientific literature Credit: Karen Arnott/EMBL-EBI In a world inundated with data, curating valuable information has never been more challenging, or more important. From academic papers…

Abstract ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels—tunnels and pores—within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement…

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…

Origin & Evolution of Life Status Report biorxiv November 6, 2023 Workflow of this study. All available coenzymes in the PDB were identified according to the CoFactor database (Fischer et al., 2010). The PDB entries of structures bound to coenzymes were downloaded programmatically through the PDBe REST API (pdbe.org/api), including…

Swati Goel, a doctoral student of Clemson’s Ph.D. in Planning, Design and the Built Environment (PDBE), recently became the Foundation for Health Environments Research (FHER) 2023-24 Griffin/McKahan/Zilm (GMZ) Graduate Fellow. The GMZ fellowship was established to encourage research related to the programming and planning of healthcare facilities and to advance…

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…

GROMACS version: GROMACS 2023.3GROMACS modification: No I am preparing files for protein-ligand simulation for PPAR alpha. The protein structure available on PDB has two truncated loops. These truncated loops introduced the artifact of long bond distances during energy minimization. If I include the loop, the system will be very large,…

Dear all, We are excited to announce two significant functionalities added to the AlphaFold Protein Structure Database (AlphaFold DB). The database has expanded since its inception in 2021 to cover over 214 million predicted structures from Google Deepmind’s AlphaFold 2 system. We now introduce sequence similarity-based search and enhanced prediction…

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…

Dear all, We are excited to inform you of some upcoming enhancements to PDBe’s ligand-related API endpoints and are seeking your valuable insights! *We are running this survey (forms.gle/agPUGCn59ffuayp57) *to collect information on two crucial points: – *Current Usage of PDBe’s Ligand-Related API Endpoints*: We want to understand which of…

We are working on aggregating and displaying all the data available for macromolecular complexes in the PDB and would like to learn more about the types of data regarding complexes that you find helpful in your research. PDBe-KB (pdbe-kb.org) is a community-driven data resource at EMBL-EBI that integrates functional annotations…

About the team/job We seek an experienced front-end developer interested in biological data to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI) to work on web services related to the Protein Data Bank in Europe (pdbe.org). This post is an exciting opportunity to work as part of EMBL-EBI…

What is abrin? In certain parts of Asia and Australia, grows a flowering plant of the bean family Fabaceae, known as Abrus precatorius, also more commonly as jequirity bean or rosary pea [1]. It’s a delicate, perennial climber but extremely invasive and classified as a weed in several countries. However, what…

September 21, 2023September 21, 2023 Swati Goel, a doctoral student of Clemson’s Ph.D. in Planning, Design and the Built Environment (PDBE), recently became the Foundation for Health Environments Research (FHER) 2023-24 Griffin/McKahan/Zilm (GMZ) Graduate Fellow. The GMZ fellowship was established to encourage research related to the programming and planning…

Description Your role This position is for an ambitious scientist, with a passion for open data, who wants to impact the development of key resources for global, public 3D-structure data. We need an inspiring and engaging person who understands the importance of teamwork and is focused on the delivery of…

Description A thriving Technical Consultancy seeks an Office Systems Application Developer to provide ongoing maintenance and development for their internal software systems. Youll be fully conversant with Microsoft Office 365 development, possess solid C# experience as well as some SQL and Windows administration experience. A competitive salary is on offer…

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…

About Speakers Followers Exhibitors Reviews Timings 09:00 AM – 06:00 PM Not Verified Add To Calendar Entry Fees Check Official Website Estimated Turnout upto 100 Delegates Editions Oct 2023 Frequency Newly Listed Claim event to edit details Overview: How to attend Competencies in Proteins: Proteins are essential for cell functions….

Dear All, We are looking for an outstanding individual to coordinate the Protein Data Bank in Europe team (PDBe; pdbe.org) team at the European Bioinformatics Institute (EMBL-EBI). This position is for an ambitious scientist, with a passion for open data, who wants to impact the development of key resources for…

We are looking for an outstanding individual to coordinate the Protein Data Bank in Europe Team (PDBe; pdbe.org) team at the European Bioinformatics Institute (EMBL-EBI). This role is central for delivering data services that significantly impact on how the scientific community uses bio-macromolecular structure data now and in the future….

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…

Scientific Database Curator – Protein Data Bank in Europe – EMBL-EBI – European Bioinformatics Institute, Hinxton Scientific Database Curator – Protein Data Bank in Europe EMBL-EBI – European Bioinformatics Institute Hinxton, United Kingdom We are seeking a structural biologist or bioinformatician with strong structural biology background and familiarity with scripting…

For decades, structural biologists have been working on cracking the molecular 3D structures of proteins to understand their function. But what if a protein doesn’t have a fixed structure? For molecules that keep changing their shape all the time, both research and sharing the findings within the scientific community can…

The Importance of Molecular Visualization and Analysis in Drug Discovery Drug discovery is a process that allows scientists to identify novel drug candidates that could eventually be approved for the treatment of a disease. There is an interesting relationship between drug discovery and the visualization of large molecular structures, such…

Closer collaborations with EMBL-EBI data resources set to further develop and grow this unique rare disease platform DECIPHER database for rare diseases joins EMBL-EBI. Credit: Karen Arnott/EMBL-EBI The DECIPHER website and database, which are used globally by researchers and clinicians to interpret and share phenotypic and genotypic data from rare…

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…

EMBL scientists contribute to developing guidelines that will facilitate sharing knowledge about unstructured proteins Coauthored with Oana Stroe For decades, structural biologists have been working on cracking the molecular 3D structures of proteins to understand their function. But what if a protein doesn’t have a fixed structure? For molecules that…

About the team/job We are looking for a software engineer specialising in search technologies (e.g. Apache Solr, Elasticsearch) with interest in biological data to join the Velankar team at the European Bioinformatics Institute (EMBL-EBI) to work on the AlphaFold Protein Structure Database (AlphaFold DB). This post is an exciting opportunity to…

A new tool for the interpretation of missense variation in humans – ProtVar – will help enable drug discovery Credit: EMBL-EBI EMBL’s European Bioinformatics Institute (EMBL-EBI) has launched ProtVar, a new web tool that helps users contextualise and interpret human missense variation within proteins. What is missense variation? Missense variation…

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…

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…

** *Dear all,* * We are excited to announce the release of the new version of the PISA software, developed at PDBe, based on the jsPISA implementation from CCP4. This new version, PISA-lite, developed in collaboration with the CCP4 core team, enables the calculation of macromolecular interaction data for every…

We have developed a new version of PISA, which focuses on analysing intermolecular interactions within existing assemblies. This updated version, named PISA-lite, generates new and enhanced PISA interaction data based on all the annotated assemblies in the PDB archive and is available in JSON format from the PDBe API. This…

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…

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…

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…

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…

An infection caused by pathogens, such as viruses, bacteria, parasites, or fungi, can be seen as a battle between the invading pathogen and our body. The role of the immune system is to protect us against disease or invading threats. But how does the body combat these intruding pathogens? To…

We have updated the tools used at PDBe and PDBe-KB for processing small molecule ligands and their interactions in the PDB archive. This process now identifies larger, linked ligands that are composed of individual components covalently linked together, allowing these molecules to be identified in a standardised manner for the…

** *Dear list, * * The AlphaFold Protein Structure Database (www.alphafold.ebi.ac.uk <www.alphafold.ebi.ac.uk>) team are excited to announce plans to expand the database’s capabilities, and we need your help with it. We seek feedback on how you perform protein similarity searches, which will help us build more effective and helpful sequence…

EMBL-EBI Associate Director for Services Jo McEntyre talks about data services to support the new EMBL Programme, open data and a new era for research assessment. EMBL-EBI’s Associate Director for Services Jo McEntyre. Credit: Carrie Tang With EMBL’s 2022-26 Programme ‘Molecules to Ecosystems’ and in line with EMBL’s Open Science policy,…

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…

According to Levinthal’s paradox, each protein may adopt around 10300 distinct structures. We now know 3-D structures for about 98% of the human proteome thanks to DeepMind’s AI system, AlphaFold. However, AlphaFold has limitations, such as its inability to generate coordinates for tiny molecules and ligands that are critical to…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

  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…

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