Update on the next RSC CICAG Open Source Tools for Chemistry workshops
PDBe Knowledge Base
This workshop explores the Protein Data Bank in Europe Knowledge Base (PDBe-KB https://www.ebi.ac.uk/pdbe/) resource and its tools for the investigation, analysis, and interpretation of biomacromolecular structures. PDBe-KB brings together data from all PDB entries and displays this data as aggregated information for individual proteins, including ligand binding sites, macromolecular interactions and more. Furthermore, this community-led resource brings together structural and functional information from a host of other related resources. In this workshop, you will learn how to use the PDBe-KB aggregated views for proteins to investigate structural and function information for proteins and their associated ligands. We will also demonstrate effective use of novel visualisation components of large-scale structural data on these pages, including 3D visualisation of superposed protein structures with their bound ligands.
2.00 PDBe-KB talk (30 min) - David Armstrong
2.30 Intro to tutorials (15 min) - David Armstrong
2.45 Break (10 min)
2.55 Intro to Biochemgraph project & ligand pages (25 min) - Preeti Choudhary
3.20 PDBe-KB ligand page design session (20 min) - Preeti Choudhary
3.40 Q&A (20 min) - David Armstrong and Preeti Choudhary
4.00 End of session
Still time to register https://www.eventbrite.com/e/open-source-tools-for-chemistry-tickets-294585512197?.
For any scientists working with biomolecules be it, medicinal chemist, structural biologist, biochemist etc. the most valuable source of primary structural information is the Protein Data Bank (PDB). This resource has now been running for 50 years so it very timely to hear about the history of the RCSB PDB and the different components that make up the repository both from a depositor and a user. The second workshop describes some of the recent changes in particular the development of Mol* a 3D viewer capable of rendering from macromolecular assemblies down to atomic details.
- History of the Protein Data Bank (PDB) and the Worldwide PDB Stephen K. Burley, RCSB Protein Data Bank
- PDBx/mmCIF Data Standard and PDB Data Deposition with OneDep Ezra Peisach and Jasmine Young
- Small Molecules in the PDB -talk + tutorial Chenghua Shao, RCSB Protein Data Bank
- OneDep Tutorial - Jasmine Young and Ezra Peisach
- wwPDB Validation: Assessing the Quality of PDB structures John Berrisford, Protein Data Bank in Europe
- How to Interpret the Quality of a PDB Structure using the wwPDB validation report - tutorial David Armstrong/John Berrisford/Jack Turner, Protein Data Bank in Europe
- 3D Visualisation of PDB Data with the Mol* viewer -James Tolchard, Protein Data Bank in Europe
- Impact of AI and Future of PDB Data: Next Generation PDB Archive - Sameer Velankar, Protein Data Bank in Europe
- Round Table Discussion - Sameer Velankar, Protein Data Bank in Europe, Stephen K. Burley, RCSB Protein Data Bank
This is part of the RSC CICAG workshops on Open Chemical Sciences, all 17 workshops are on the RSC CICAG YouTube playlist https://www.youtube.com/playlist?list=PLBQwbn0mPhvWfOx6ce_vUjr54ftLBmSH0.
If you have any suggestions (or would like to volunteer) for future workshops feel free to get in touch.
Registration for the November RSC CICAG workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)
Given that it is the 50th anniversary of the PDB archive it is appropriate that the two final workshops for 2021 are describing this absolutely invaluable resource.
Protein Data Bank Workshop (16 November 2021 15.00 – 17.00 GMT)
The Protein Data Bank https://www.wwpdb.org archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that help students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Open access PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine. The PDB is a vast resource and this workshop will be invaluable to anyone seeking to get full value from the PDB.
Mol* Workshop (18 November 2021 15.00 – 17.00 GMT)
Mol* is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data. More information can be found here: https://molstar.org. High-performance graphics and data handling of the Mol* Viewer allow users to simultaneously visualise up to hundreds of (superimposed) protein structures, play molecular dynamics trajectories, render cell-level models at atomic detail with tens of millions of atoms, or display huge models obtained by I/HM such as the Nuclear Pore Complex.
David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; DOI.
If you want to learn more about the history of the PDB there is a video here.
These workshops are sponsored by Liverpool ChiroChem
QuickLookProtein is a macOS Quick Look extension to preview protein/3D structure files (PDB, SDF, CIF).
It works in all places where macOS uses Quick Look, e.g. in Finder and Spotlight. In Finder, just select the protein structure file and press Space to open Quick Look.
The rendering of the 3D structure is performed using 3Dmol.js.
The extension is packaged into a main app, whose purpose is to set a few settings used for the display of the 3D models. QuickLookProtein requires macOS Big Sur (version 11.0+).
ISOLDE 1.2.0 is available, and ready to install for @UCSFChimeraX 1.2! As usual, just get the ChimeraX 1.2 release from https://www.rbvi.ucsf.edu/chimerax/download.html then install ISOLDE via "Tools/More Tools. Code is on GitHub https://github.com/tristanic/isolde.
ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments.
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and personal use.
You can view snapshot here https://twitter.com/CrollTristan/status/1390709520876331009
The PDB in Europe have just introduced a new viewer for biomolecules, Mol*, is a new 3D molecular viewer developed in collaboration between RCSB PDB, PDBe, and CEITEC, from RCSB PDB and PDBe pages.
On the PDBe pages, Mol* has now replaced the LiteMol viewer in all instances, including on the PDBe search and entry pages e.g. pdbe.org/5lnk/3d. Access Mol* from any 3D View tab for Structure Summary pages at RCSB.org. Both the LiteMol and NGL viewers at PDBe and RCSB PDB, respectively, will no longer be actively developed.
Here is the structure of Aldehyde Oxidase PDB ID 4uhw.
First let me say I’m not a big Fortran user but any blog posts about Fortran always seem to be very popular, and the Fortran on a Mac page is one of the most frequently read. I've just been sent details of another Fortran program and I've added it to the page.
Illustrate is a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. It is used to create the RCSB Molecule of the month.
At the latest Bio-ITWorld 3decision was recognised with an award
3decision – next generation structural knowledge management solution
Although wildly used, rational structure-based drug design (SBDD) techniques are far from being applied to their fullest potential. The major hurdles lie in the inconsistent data persistence and the complexity of analyzing structural data. Moreover, the structural data is often analyzed by domain experts only and their knowledge and experience are not well shared and exposed to other communities. Abbvie has addressed these pitfalls by co-developing a web-based structural knowledge management solution called 3decision. It allows Abbvie to transform a massive amount of data coming from in-house and public 3D structures and sequences, into applicable knowledge for drug discovery projects. The collaborative aspects within SBDD projects are in focus and the user interface allows all types of users to easily generate, test and connect their ideas with each other. The development of 3decision allowed Abbvie to dramatically increases the ROI of SBDD work and protein structure production.
3decision is a web-based collaborative platform for storing, analyzing and sharing protein-ligand structures, sequences, and associated data, it works fine on a Mac and Google Chrome is recommended browser