Opioids and Pain Signaling (from PDB-101) RCSBProteinDataBank 2021-06-22 | Pain is one of the most trying experiences of life. On the cellular level it is communicated via special neuronal pathways. On the molecular level, however, pain is communicated like any other sensation, via a set of electrical and chemical signals facilitated by complex molecular machinery. These signals can be modulated by opioids, causing us to feel less pain, or no pain at all. Learn how opioids activate the G-proteins which in turn interact with other proteins to edit the pain signal. Video Guide: 00:06 Pain signaling: 00:25 Electrical Signals: Action Potential 02:47 Chemical Signals: Synaptic Signaling04:08 Modulation of pain signal by opioids: 04:33 Introduction to opioid receptor (GPCR) and G protein 05:22 G-beta-gamma interactions 05:58 G-alpha interactions 07:09 Blocking the effects of opioids: the mechanism of NaloxoneVisit pdb101.rcsb.org/browse/drugs-and-the-brain to explore more educational resources on how drugs help tune the function of the brain and nervous system.
Preparing the development environment for Python Scripting for Molecular Docking Crash Course RCSBProteinDataBank 2024-09-13 | This video will help you set up your development environment for the course.In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).Full course on PDB-101 with additional development environment set up instructions: pdb101.rcsb.org/train/training-events/python3
Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (July30, 2024 Wbinar) RCSBProteinDataBank 2024-09-13 | In the second edition of this webinar SARS-CoV-2 Main Protease is used to introduce and reinforce the use of RCSB.org resources for teaching protein structure and function.After watching this webinar you will be able to:– Understand the types of 3D structural data hosted on RCSB.org (experimental and computational)– Navigate the RCSB PDB website to visualize each 3D structure and explore various annotations mapped to it– Compare the shapes, interactions and functions of groups of PDB structure with similar sequences and/or similar structures – Use RCSB PDB data, tools and resources to enhance classroom instructions and build lessons for teaching about enzymesVideo Sections:0:00 Introduction to the Protein Data Bank and SARS-CoV-211:21 Exploring the SARS-CoV-2 Main Protease structure using RCSB.org46:04 Making connections using RCSB.org 1:25:09 Discussion and Q&A
Python Scripting for Molecular Docking: Docking with AutoDock Vina RCSBProteinDataBank 2024-09-13 | In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions: pdb101.rcsb.org/train/training-events/python3If you have little or no prior coding experience with Python, you are encouraged to go through the two previous PDB-101 courses on Python:Python Scripting for Biochemistry & Molecular Biology | Part 1 (pdb101.rcsb.org/train/training-events/python)Python Scripting for Biochemistry & Molecular Biology | Part 2 (pdb101.rcsb.org/train/training-events/python2)
Python Scripting for Molecular Docking: Docking Preparation RCSBProteinDataBank 2024-09-13 | In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions: pdb101.rcsb.org/train/training-events/python3If you have little or no prior coding experience with Python, you are encouraged to go through the two previous PDB-101 courses on Python:Python Scripting for Biochemistry & Molecular Biology | Part 1 (pdb101.rcsb.org/train/training-events/python)Python Scripting for Biochemistry & Molecular Biology | Part 2 (pdb101.rcsb.org/train/training-events/python2)
Python Scripting for Molecular Docking: Manipulating Molecules with RDKit RCSBProteinDataBank 2024-09-13 | In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions: pdb101.rcsb.org/train/training-events/python3If you have little or no prior coding experience with Python, you are encouraged to go through the two previous PDB-101 courses on Python:Python Scripting for Biochemistry & Molecular Biology | Part 1 (pdb101.rcsb.org/train/training-events/python)Python Scripting for Biochemistry & Molecular Biology | Part 2 (pdb101.rcsb.org/train/training-events/python2)
Python Scripting for Molecular Docking: Enzyme Commission Class with Ligands RCSBProteinDataBank 2024-09-13 | In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions: pdb101.rcsb.org/train/training-events/python3If you have little or no prior coding experience with Python, you are encouraged to go through the two previous PDB-101 courses on Python:Python Scripting for Biochemistry & Molecular Biology | Part 1 (pdb101.rcsb.org/train/training-events/python)Python Scripting for Biochemistry & Molecular Biology | Part 2 (pdb101.rcsb.org/train/training-events/python2)
A Deep Dive into Computed Structure Model Exploration at RCSB.org RCSBProteinDataBank 2024-05-20 | Learn how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structures. Two case studies are provided: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1) and Class II aminoacyl-tRNA synthetases.Presentation slides and more information at pdb101.rcsb.org/train/training-events/csm2Video Sections: 0:00 Welcome and Introduction to the PDB and course content2:50 Case Study 1: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1)15:30 Case Study 2: Class II Aminoacyl-tRNA Synthetases46:14 Q&A
Understanding PDB Validation: Which experimental structures should I rely on? RCSBProteinDataBank 2024-05-20 | Learn about primary PDB structure quality metrics, including those in the validation slider graphic; how PDB structure quality varies across the archive; and identify good structure(s) for research from RCSB.org.Presentation slides and more information at pdb101.rcsb.org/train/training-events/validationVideo sections:Introduction:0:00 Protein Data Bank (PDB) and Quality Variation of StructuresUnderstanding PDB Validation: Which experimental structures should I rely on:5:38 wwPDB Validation Overview13:22 Validation of chemical geometry for PDB structures determined by all methods17:08 Validation of macromolecular crystallography (MX) structures23:27 Validation of 3D electron microscopy (3DEM) structures29:41 RCSB.org access to validation reports and quality review in 3D31:44 RCSB.org structure confidence review in 3D33:53 RCSB.org interactive ligand quality review43:47 Q&A
Building and Animating Catalase in a High School Classroom RCSBProteinDataBank 2024-04-09 | AP Biology students at John H. Pitman High School were tasked with creating animations depicting an active site in catalase and the mechanistic breakdown of two hydrogen peroxide molecules. These animations were created using pipe cleaners, clay, toothpicks, and stop-motion cinematography. The data used to generate these animations were from RCSB Protein Data Bank resources, AlphaFold DB, and various scientific publications. Read the Education Corner article to find out more and to download the lesson plan for the classroom activity described at cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/corner.html
Visualize Biomolecular structures with Mol*: From Atoms to Movies RCSBProteinDataBank 2024-02-22 | Mol* (MolStar) is a tool is freely available on RCSB.org for visualizing biomolecular structures in 3D. After watching this webinar, you will be able to:1. Visualize 3D structural data from experimentally determined structures deposited to Protein Data Bank and computed structure models from sources such as AlphaFold2. Select all or parts of the 3D structure to display it in different representations, colors, and more, to analyze interactions, and to measure distances and angles within and between proteins, nucleic acids, and other molecules3. Map information to available structures such as functional features or mutations4. Superimpose structures of the same protein in different conformations or similar proteins to compare features5. Export publication quality images and animations for videos
Immunology and Cancer 3: Immune Checkpoints: Biology and Therapeutic Strategies (from PDB-101) RCSBProteinDataBank 2024-02-02 | This three-part series explores the human immune response to cancer focusing on cellular and molecular details of the process. Part 1 showcases the process of antigen harvesting by dendritic cells and later the T-cell maturation process. Part 2 focuses on T-cell activation and demonstrates the mechanisms by which the immune system destroys the cancer cells. Part 3 focuses on the immune checkpoints - a mechanism by which the immune system terminates the immune response and later describes the immune checkpoint therapies used in cancer treatment.Video Guide0:05 Introduction to immune checkpoints0:17 Secondary signal inhibition at the dendritic cell/T-cell synapse 0:58 Primary signal inhibition in Killer T-cells by PD-1/PDL-1 interaction1:50 Tumor formation and metastasis2:03 Introduction to immune checkpoints therapies and monoclonal antibodies2:21 Restoration of the secondary signal at the dendritic cell/T-cell synapse by monoclonal antibodies2:34 Restoration of Killer T-cell action by monoclonal antibodies2:45 Monoclonal antibody cocktailsVideo CreditsStory byEthan Cartagena (Spring 2022 RCSB PDB Intern)Story SupportSteven C. Almo (Albert Einstein College of Medicine), Stephen K. Burley (RCSB PDB), Paul Craig (RIT), David Goodsell (RCSB PDB), and Maria Voigt (RCSB PDB)Animation and Video EditingMaria Voigt (RCSB PDB)NarrationEmma Chavez (Summer 2022 RCSB PDB Intern)SoundsPixabay.comLearn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancerThis video features experimental structures from the Protein Data Bank along with Computed Structure Models from the AlphaFold DB. Visit rcsb.org to explore these structures in 3D. MHC class I: 1HSA, AF_AFP01889F1T-cell Receptor: 1TCR, 2HACCD8 Co-receptor: 1AKJ, AF_AFP01732F1B7/CTLA-4 Complex: 1I8L, 1I85B7: AF_AFP42081F1CTLA-4: AF_AFP16410F1Monoclonal Antibody/MHC class I Antigen Complex: 3UO1PD-1 in Complex with Monoclonal Antibody: 5GGSPD1: AF_AFQ15116F1PD-1/PD-L1 Complex: 3BIK PD-L1: AF_AFQ9NZQ7F1Immunoglobulin: 1IGT
Immunology and Cancer 2: T-cell Activation and Action (from PDB-101) RCSBProteinDataBank 2024-02-02 | This three-part series explores the human immune response to cancer focusing on cellular and molecular details of the process. Part 1 showcases the process of antigen harvesting by dendritic cells and later the T-cell maturation process. Part 2 focuses on T-cell activation and demonstrates the mechanisms by which the immune system destroys the cancer cells. Part 3 focuses on the immune checkpoints - a mechanism by which the immune system terminates the immune response and later describes the immune checkpoint therapies used in cancer treatment.Video Guide0:09 Primary signal in Killer and Helper T-cell activation 0:32 Secondary signal in T-cell activation 0:45 T-cells proliferation1:11 Killer T-cell action – destruction of cancer cells1:38 Helper T-cell action – activation of B-cells and MacrophagesVideo CreditsStory byEthan Cartagena (Spring 2022 RCSB PDB Intern)Story SupportSteven C. Almo (Albert Einstein College of Medicine), Stephen K. Burley (RCSB PDB), Paul Craig (RIT), David Goodsell (RCSB PDB), and Maria Voigt (RCSB PDB)Animation and Video EditingMaria Voigt (RCSB PDB)NarrationEmma Chavez (Summer 2022 RCSB PDB Intern)SoundsPixabay.comLearn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancerThis video features experimental structures from the Protein Data Bank along with Computed Structure Models from the AlphaFold DB. Visit rcsb.org to explore these structures in 3D. MHC class I: 1HSA, AF_AFP01889F1T-cell Receptor: 1TCR, 2HACCD8 Co-receptor: 1AKJ, AF_AFP01732F1B7/CTLA-4 Complex: 1I8L, 1I85B7: AF_AFP42081F1CTLA-4: AF_AFP16410F1Interleukin-2 Receptor: 2ERJ, AF_AFP01589F1, AF_AFP14784F1, AF_AFP31785F1Perforin: 6SB3, 8A1DGranzyme: 2ZGCAntibody/MHC class I Antigen Complex: 3UO1Immunoglobulin: 1IGT
Immunology and Cancer 1: Dendritic Cells, Antigens, and T-cell Maturation (from PDB-101) RCSBProteinDataBank 2024-02-02 | This three-part series explores the human immune response to cancer focusing on cellular and molecular details of the process. Part 1 showcases the process of antigen harvesting by dendritic cells and later the T-cell maturation process. Part 2 focuses on T-cell activation and demonstrates the mechanisms by which the immune system destroys the cancer cells. Part 3 focuses on the immune checkpoints - a mechanism by which the immune system terminates the immune response and later describes the immune checkpoint therapies used in cancer treatment.Video Guide0:06 Immune system introduction0:20 Dendritic cell introduction0:40 Antigen/neoantigen harvesting and processing by dendritic cells1:05 Major Histocompatibility Complex I and II introduction1:49 T-cells maturation in the thymus and generation of T-cell receptor2:32 T-cell receptor testing for “self” antigens and elimination2:50 T-cell differentiation into Helper and Killer types (CD4/CD8 Co receptors)3:19 Initial steps in T-cell activationVideo CreditsStory byEthan Cartagena (Spring 2022 RCSB PDB Intern)Story SupportSteven C. Almo (Albert Einstein College of Medicine), Stephen K. Burley (RCSB PDB), Paul Craig (RIT), David Goodsell (RCSB PDB), and Maria Voigt (RCSB PDB)Animation and Video EditingMaria Voigt (RCSB PDB)NarrationEmma Chavez (Summer 2022 RCSB PDB Intern)SoundsPixabay.comLearn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancerThis video features experimental structures from the Protein Data Bank along with Computed Structure Models from the AlphaFold DB. Visit rcsb.org to explore these structures in 3D. MHC class I: 1HSA, AF_AFP01889F1MHC class II: 1DLH, AF_AFP01903F1, AF_AFP01911F1T-cell receptor: 1TCR, 2HACCD8 Co-receptor: 1AKJ, AF_AFP01732F1CD4 Co-receptor: 1JL4, AF_AFP01730F1RAG1/2 Recombinase: 4WWXSerine Protease: 4Q80
Seasons Greetings from the RCSB PDB RCSBProteinDataBank 2023-12-21 | Celebrate the holidays with PDB-themed wrapping paper/virtual meeting backgrounds. Visit pdb101.rcsb.org/news/656e3114d78e004e766a96c3 to learn more about the proteins used in this animation and download the resources.
Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning Part 2 RCSBProteinDataBank 2023-10-23 | In this guided session, you will work with an example of a typical workflow that integrate Data and Search APIs and then apply the knowledge to your own specific problem.Please visit the PDB-101 Training Course page for access to the slides, documents, and other training materials: pdb101.rcsb.org/train/training-events/apiWho Should Attend* Bioinformatics or structural biology researchers* Researchers that need to cross-reference PDB and data from other resources* Anyone interested in large scale analyses of structural data (experimental or computational)
Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning RCSBProteinDataBank 2023-10-12 | The lectures in this session will introduce you to the two main RCSB PDB APIs: Data API and Search API.Please visit the PDB-101 Training Course page for access to the slides, documents, and other training materials: pdb101.rcsb.org/train/training-events/apiTimestamps:00:00:00 Welcome00:07:55 Introduction to RCSB PDB APIs and data schemas00:37:59 Data API01:09:10 Search API01:41:36 Search and Data API hands-on teaserAfter completion of this session, you will* Understand the data structure and its relation to the PDBx/mmCIF dictionary and external data* Become familiarized with the two available interfaces in the Data API: GraphQL and REST* Write search queries with one or multiple search conditions to find PDB identifiers* Be familiar with search services beyond text: sequence, seqmotif, structure, chemical, strucmotif* Become acquainted with the Python client for Search API
Evolution of the Insulin Gene RCSBProteinDataBank 2023-08-31 | This video introduces you to insulin family proteins and the evolution of the insulin gene.
Molecular Machinery: A Tour RCSBProteinDataBank 2023-08-29 | This video introduces the Molecular Machinery interactive poster available from PDB-101 at cdn.rcsb.org/pdb101/molecular-machinery/.
Insulin Biosynthesis RCSBProteinDataBank 2023-08-18 | This video describes how insulin is made in pancreatic beta cells and processed to form the functional molecule.0:00 Insulin Biosynthesis0:31 What is Insulin?1:40 Pre-pro-insulin3:39 Summary
What is Cancer? RCSBProteinDataBank 2023-06-27 | This video discusses what cancer is, why we have cancer, how it is diagnosed and treated.Chapters0:00 A Cancer Expert Talks to Students0:18 What is Cancer?2:40 Maintaining Balance4:14 Cell growth and Cancer7:40 Autonomous and Immortal8:25 Diagnosis of Cancer9:00 Classification and Treatment
Breast Cancer Chess Championship: Trastuzumab vs HER2 Receptor RCSBProteinDataBank 2023-05-16 | Winner of the Judge’s Award First Place and Viewer's Choice Award in the 2023 RCSB PDB Video Challenge for High School Students “Molecular Mechanisms of Targeted Cancer Therapies”By Joan Ashreya Mare, Grace Lee, and Ananya VakkalankaWest Windsor-Plainsboro High School South, West Windsor, New JerseyTeam Advisor: Mrs. Meenakshi BhattacharyaVisit pdb101.rcsb.org to learn more
Fighting Cancer by Targeting G12C RCSBProteinDataBank 2023-05-16 | Winner of the Judge’s Award Second Place in the 2023 RCSB PDB Video Challenge for High School Students “Molecular Mechanisms of Targeted Cancer Therapies”By Amanda Nguyen, Kristen Ngo, and Gavin GonzalesMira Mesa High School, San Diego, CATeam Advisor: Mrs. Lisa YonedaVisit pdb101.rcsb.org to learn more
Investigating the Role of VEGF in Targeted Therapy for Cancer RCSBProteinDataBank 2023-05-16 | Winner of the Judge’s Award Third Place in the 2023 RCSB PDB Video Challenge for High School Students “Molecular Mechanisms of Targeted Cancer Therapies”By Victoria SilvaJericho High School, Jericho, NYTeam Advisor: Mrs. Samantha SforzaVisit pdb101.rcsb.org to learn more
Understanding PDBx/mmCIF: Course Introduction RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Stephen K. Burley, Director, RCSB Protein Data Bank
Introduction and course objectives RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Gregg Crichlow, Biocurator, RCSB PDB, Rutgers University
PDBx/mmCIF format - Not your parents’ legacy PDB format RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Ezra Peisach, Scientific Software Developer/PDBx mmCIF Dictionary Manager
PDBx/mmCIF data files - Lifting the lid off the black box RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Brian Hudson, Biocurator, RCSB PDB, Rutgers University
Programmatic data access and analysis using PDBx/mmCIF files, Part 1 RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Irina Persikova, Biocuration Lead Deputy, RCSB PDB, Rutgers University
Programmatic data access and analysis using PDBx/mmCIF files, Part 2 RCSBProteinDataBank 2023-05-09 | This course is designed to help users understand the basics of PDBx/mmCIF data dictionary and file format that underpin the archiving of experimentally determined three-dimensional biostructures in the PDB. After completing of this course, you will be able to use software tools for generating, editing, and visualizing PDBx/mmCIF files, understand PDBx/mmCIF dictionary extensions (including ModelCIF for computed structure models), and parse data from PDBx/mmCIF files for your research.Access the full course and supplementary materials at pdb101.rcsb.org/train/training-events/mmcif.Presenter:Chenghua Shao, Biocurator, Scientific Software Developer/KPI Evaluator, RCSB PDB, Rutgers University
Python Scripting for Biochemistry &Molecular Biology - Part 2 Introduction RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data.Access the full course: Part 1:pdb101.rcsb.org/train/training-events/pythonPart 2:pdb101.rcsb.org/train/training-events/python2
Python Primer: Review of Python and the Jupyter Notebook environment RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. Access the full course: Part 1: pdb101.rcsb.org/train/training-events/python Part 2: pdb101.rcsb.org/train/training-events/python2
Nonlinear regression: Creating the Pandas DataFrame RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. Access the full course: Part 1: pdb101.rcsb.org/train/training-events/python Part 2: pdb101.rcsb.org/train/training-events/python2
Nonlinear Regression: Curve Fitting RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. Access the full course: Part 1: pdb101.rcsb.org/train/training-events/python Part 2: pdb101.rcsb.org/train/training-events/python2
Extracting data from mmCIF files using the Biopython library RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. Access the full course: Part 1: pdb101.rcsb.org/train/training-events/python Part 2: pdb101.rcsb.org/train/training-events/python2
Extracting data from mmCIF files using the RCSB PDB API RCSBProteinDataBank 2023-05-04 | This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. Access the full course: Part 1: pdb101.rcsb.org/train/training-events/python Part 2: pdb101.rcsb.org/train/training-events/python2
Multiple Views in a Mol* Session RCSBProteinDataBank 2023-02-14 | This video shows how to create, save, and open Mol* sessions with multiple saved views. Share saved sessions with students or with researchers for collaboration.Learn more about using Mol* at rcsb.org/docs/3d-viewers/mol*/getting-started
Exploring the PD-1/PD-L1 pathway using Data, Tools, and Resources from RCSB.org RCSBProteinDataBank 2023-02-08 | Based on case studies presented in http://doi.org/10.1002/pro.448200:00: Intro to PD-1/PD-L101:45: Exploring PDB ID 5jxe - Structure Summary page04:35 How Pembrolizumab Disrupts PD-1:PD-L1 Binding 05:40 Compare structures07:28 Other Therapeutic Anti-PD-1 AntibodiesLearn more about Pembrolizumab (pdb101.rcsb.org/motm/204) and other cancer therapy approaches on PDB-101 (pdb101.rcsb.org/).
Introduction to Python and to Jupyter Notebooks RCSBProteinDataBank 2023-01-26 | Lesson 1/4 of "Python Scripting for Biochemistry & Molecular Biology" Crash Course.This workshop makes the life scientists acquaintant with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation.
Reading and Writing Files using Python and Jupiter Notebooks RCSBProteinDataBank 2023-01-26 | Lesson 2/4 of workshop "Python Scripting for Biochemistry & Molecular Biology".This workshop makes the life scientists acquaintant with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation.
Processing Multiple Files RCSBProteinDataBank 2023-01-26 | Lesson 3/4 of the workshop "Python Scripting for Biochemistry & Molecular Biology".This workshop makes the life scientists acquaintant with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation.
Visualizing PDB structures in the Jupyter Notebooks RCSBProteinDataBank 2023-01-26 | Python Scripting for Biochemistry & Molecular Biology.This workshop makes the life scientists acquaintant with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation.
Seasons Greetings from the RCSB PDB RCSBProteinDataBank 2022-12-22 | A major 2022 RCSB.org release was a feature that enables users to explore Computed Structure Models (CSMs) alongside experimentally-determined structures from the PDB archive (rcsb.org/news/6304ee57707ecd4f63b3d3db).This animation celebrates this milestone by highlighting PDB structure 7VMF (rcsb.org/structure/7VMF), a histone acetyltransferase from Arabidopsis thaliana in dark blue. The CSM (rcsb.org/structure/AF_AFQ56WH4F1) created based on the corresponding UniProt sequence Q56WH4 (rcsb.org/groups/sequence/polymer_entity/Q56WH4) is then displayed with high confidence regions shown in ribbon representation in cyan and lower confidence regions shown in ball and stick representation.
Accessing Experimental Structures from the PDB RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Dennis Piehl, Ph.D. - RCSB Protein Data Bank, Rutgers University Title: Accessing Experimental Structures from the PDB
Making the Best use of Protein Structure Data in KBase and PDB RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Christopher Henry, Ph.D. - KBase, Argonne National LaboratoryTitle: Making the Best use of Protein Structure Data in KBase and PDB
KBase Apps for Protein Structure Data Communication and Integration with RCSB PDB RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Qizhi Zhang, Ph.D. - KBase, Argonne National Laboratory Title: KBase Apps for Protein Structure Data Communication and Integration with RCSB PDB
Introduction to Mol* (MolStar) Molecular Graphics System RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Shuchismita Dutta, Ph.D. - RCSB Protein Data Bank, Rutgers University Title: Introduction to the Virtual Crash Course on Using KBase to access PDB Structures and Computed Structure Models
Accessing Computed Structure Models generated using AlphaFold2 or RoseTTAFold(2) RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Brinda Vallat, Ph.D. - RCSB Protein Data Bank, Rutgers University Title: Accessing Computed Structure Models generated using AlphaFold2 or RoseTTAFold(2)
Protein Candidates from Function Queries in KBase RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Janaka N. Edirisinghe, Ph.D. - KBase, Argonne National Laboratory Title: Protein Candidates from Function Queries in KBase
KBase/RCSB PDB Crash Course Objectives RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Christopher Henry, Ph.D. - KBase, Argonne National Laboratory Title: Review of Joint DOE KBase/RCSB PDB Crash Course Objectives
Introduction | Using KBase to Access Protein Structures and Models RCSBProteinDataBank 2022-11-29 | A virtual course ‘Using KBase to access PDB Structures and Computed Structure Models’ was held on Thursday November 10, 2022. The participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. The talk synopses and the summary of the Q and A are available here:https://go.rutgers.edu/88xapxdeUse this link to access the full courseyoutube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0Presenter: Stephen K. Burley, Director, RCSB Protein Data Bank Title: Introduction to the Virtual Crash Course on Exploring the Computed Structure Models on RCSB.org
