RCSBProteinDataBank
Neuronal Signaling and Sodium-Potassium Pump (from PDB-101)
updated
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
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 enzymes
Video Sections:
0:00 Introduction to the Protein Data Bank and SARS-CoV-2
11:21 Exploring the SARS-CoV-2 Main Protease structure using RCSB.org
46:04 Making connections using RCSB.org
1:25:09 Discussion and Q&A
Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions:
pdb101.rcsb.org/train/training-events/python3
If 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)
Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions:
pdb101.rcsb.org/train/training-events/python3
If 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)
Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions:
pdb101.rcsb.org/train/training-events/python3
If 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)
Full course on PDB-101 with links to corresponding Jupyter Notebooks and development environment set up instructions:
pdb101.rcsb.org/train/training-events/python3
If 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)
Presentation slides and more information at pdb101.rcsb.org/train/training-events/csm2
Video Sections:
0:00 Welcome and Introduction to the PDB and course content
2:50 Case Study 1: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1)
15:30 Case Study 2: Class II Aminoacyl-tRNA Synthetases
46:14 Q&A
Presentation slides and more information at pdb101.rcsb.org/train/training-events/validation
Video sections:
Introduction:
0:00 Protein Data Bank (PDB) and Quality Variation of Structures
Understanding PDB Validation: Which experimental structures should I rely on:
5:38 wwPDB Validation Overview
13:22 Validation of chemical geometry for PDB structures determined by all methods
17:08 Validation of macromolecular crystallography (MX) structures
23:27 Validation of 3D electron microscopy (3DEM) structures
29:41 RCSB.org access to validation reports and quality review in 3D
31:44 RCSB.org structure confidence review in 3D
33:53 RCSB.org interactive ligand quality review
43:47 Q&A
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
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 AlphaFold
2. 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 molecules
3. Map information to available structures such as functional features or mutations
4. Superimpose structures of the same protein in different conformations or similar proteins to compare features
5. Export publication quality images and animations for videos
Video Guide
0:05 Introduction to immune checkpoints
0:17 Secondary signal inhibition at the dendritic cell/T-cell synapse
0:58 Primary signal inhibition in Killer T-cells by PD-1/PDL-1 interaction
1:50 Tumor formation and metastasis
2:03 Introduction to immune checkpoints therapies and monoclonal antibodies
2:21 Restoration of the secondary signal at the dendritic cell/T-cell synapse by monoclonal antibodies
2:34 Restoration of Killer T-cell action by monoclonal antibodies
2:45 Monoclonal antibody cocktails
Video Credits
Story by
Ethan Cartagena (Spring 2022 RCSB PDB Intern)
Story Support
Steven 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 Editing
Maria Voigt (RCSB PDB)
Narration
Emma Chavez (Summer 2022 RCSB PDB Intern)
Sounds
Pixabay.com
Learn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancer
This 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_AFP01889F1
T-cell Receptor: 1TCR, 2HAC
CD8 Co-receptor: 1AKJ, AF_AFP01732F1
B7/CTLA-4 Complex: 1I8L, 1I85
B7: AF_AFP42081F1
CTLA-4: AF_AFP16410F1
Monoclonal Antibody/MHC class I Antigen Complex: 3UO1
PD-1 in Complex with Monoclonal Antibody: 5GGS
PD1: AF_AFQ15116F1
PD-1/PD-L1 Complex: 3BIK
PD-L1: AF_AFQ9NZQ7F1
Immunoglobulin: 1IGT
Video Guide
0:09 Primary signal in Killer and Helper T-cell activation
0:32 Secondary signal in T-cell activation
0:45 T-cells proliferation
1:11 Killer T-cell action – destruction of cancer cells
1:38 Helper T-cell action – activation of B-cells and Macrophages
Video Credits
Story by
Ethan Cartagena (Spring 2022 RCSB PDB Intern)
Story Support
Steven 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 Editing
Maria Voigt (RCSB PDB)
Narration
Emma Chavez (Summer 2022 RCSB PDB Intern)
Sounds
Pixabay.com
Learn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancer
This 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_AFP01889F1
T-cell Receptor: 1TCR, 2HAC
CD8 Co-receptor: 1AKJ, AF_AFP01732F1
B7/CTLA-4 Complex: 1I8L, 1I85
B7: AF_AFP42081F1
CTLA-4: AF_AFP16410F1
Interleukin-2 Receptor: 2ERJ, AF_AFP01589F1, AF_AFP14784F1, AF_AFP31785F1
Perforin: 6SB3, 8A1D
Granzyme: 2ZGC
Antibody/MHC class I Antigen Complex: 3UO1
Immunoglobulin: 1IGT
Video Guide
0:06 Immune system introduction
0:20 Dendritic cell introduction
0:40 Antigen/neoantigen harvesting and processing by dendritic cells
1:05 Major Histocompatibility Complex I and II introduction
1:49 T-cells maturation in the thymus and generation of T-cell receptor
2:32 T-cell receptor testing for “self” antigens and elimination
2:50 T-cell differentiation into Helper and Killer types (CD4/CD8 Co receptors)
3:19 Initial steps in T-cell activation
Video Credits
Story by
Ethan Cartagena (Spring 2022 RCSB PDB Intern)
Story Support
Steven 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 Editing
Maria Voigt (RCSB PDB)
Narration
Emma Chavez (Summer 2022 RCSB PDB Intern)
Sounds
Pixabay.com
Learn more about the molecular biology of Cancer on PDB-101: pdb101.rcsb.org/browse/cancer
This 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_AFP01889F1
MHC class II: 1DLH, AF_AFP01903F1, AF_AFP01911F1
T-cell receptor: 1TCR, 2HAC
CD8 Co-receptor: 1AKJ, AF_AFP01732F1
CD4 Co-receptor: 1JL4, AF_AFP01730F1
RAG1/2 Recombinase: 4WWX
Serine Protease: 4Q80
Visit pdb101.rcsb.org/news/656e3114d78e004e766a96c3 to learn more about the proteins used in this animation and download the resources.
Please visit the PDB-101 Training Course page for access to the slides, documents, and other training materials: pdb101.rcsb.org/train/training-events/api
Who 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)
Please visit the PDB-101 Training Course page for access to the slides, documents, and other training materials: pdb101.rcsb.org/train/training-events/api
Timestamps:
00:00:00 Welcome
00:07:55 Introduction to RCSB PDB APIs and data schemas
00:37:59 Data API
01:09:10 Search API
01:41:36 Search and Data API hands-on teaser
After 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
0:00 Insulin Biosynthesis
0:31 What is Insulin?
1:40 Pre-pro-insulin
3:39 Summary
Chapters
0:00 A Cancer Expert Talks to Students
0:18 What is Cancer?
2:40 Maintaining Balance
4:14 Cell growth and Cancer
7:40 Autonomous and Immortal
8:25 Diagnosis of Cancer
9:00 Classification and Treatment
By Joan Ashreya Mare, Grace Lee, and Ananya Vakkalanka
West Windsor-Plainsboro High School South, West Windsor, New Jersey
Team Advisor: Mrs. Meenakshi Bhattacharya
Visit pdb101.rcsb.org to learn more
By Amanda Nguyen, Kristen Ngo, and Gavin Gonzales
Mira Mesa High School, San Diego, CA
Team Advisor: Mrs. Lisa Yoneda
Visit pdb101.rcsb.org to learn more
By Victoria Silva
Jericho High School, Jericho, NY
Team Advisor: Mrs. Samantha Sforza
Visit pdb101.rcsb.org to learn more
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
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
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
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
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
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
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Access the full course:
Part 1:
pdb101.rcsb.org/train/training-events/python
Part 2:
pdb101.rcsb.org/train/training-events/python2
Learn more about using Mol* at rcsb.org/docs/3d-viewers/mol*/getting-started
00:00: Intro to PD-1/PD-L1
01:45: Exploring PDB ID 5jxe - Structure Summary page
04:35 How Pembrolizumab Disrupts PD-1:PD-L1 Binding
05:40 Compare structures
07:28 Other Therapeutic Anti-PD-1 Antibodies
Learn more about Pembrolizumab (pdb101.rcsb.org/motm/204) and other cancer therapy approaches on PDB-101 (pdb101.rcsb.org/).
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.
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.
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.
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.
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.
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Dennis Piehl, Ph.D. - RCSB Protein Data Bank, Rutgers University
Title: Accessing Experimental Structures from the PDB
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Christopher Henry, Ph.D. - KBase, Argonne National Laboratory
Title: Making the Best use of Protein Structure Data in KBase and PDB
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Qizhi Zhang, Ph.D. - KBase, Argonne National Laboratory
Title: KBase Apps for Protein Structure Data Communication and Integration with RCSB PDB
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: 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
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Brinda Vallat, Ph.D. - RCSB Protein Data Bank, Rutgers University
Title: Accessing Computed Structure Models generated using AlphaFold2 or RoseTTAFold(2)
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Janaka N. Edirisinghe, Ph.D. - KBase, Argonne National Laboratory
Title: Protein Candidates from Function Queries in KBase
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Christopher Henry, Ph.D. - KBase, Argonne National Laboratory
Title: Review of Joint DOE KBase/RCSB PDB Crash Course Objectives
The talk synopses and the summary of the Q and A are available here:
https://go.rutgers.edu/88xapxde
Use this link to access the full course
youtube.com/playlist?list=PLHib7JgKNUUf8Z8jSK57FsJrms94wpaL0
Presenter: Stephen K. Burley, Director, RCSB Protein Data Bank Title: Introduction to the Virtual Crash Course on Exploring the Computed Structure Models on RCSB.org