RCSBProteinDataBank
What is a Protein? (from PDB-101)
updated
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
Title: Introduction to the Virtual Crash Course on Exploring the Computed Structure Models on RCSB.org
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
Brinda Vallat
Scientific Software Developer/PDB-Dev Representative and ModelCIF Manager
RCSB PDB/Rutgers
________
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
Shuchismita Dutta
Scientific Educational Development Lead and Documentation Lead
RCSB PDB/Rutgers
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
Joan Segura
Scientific Software Developer, RCSB PDB/UCSD
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
Chenghua Shao
Scientific Software Developer/KPI Evaluator
RCSB PDB/Rutgers
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
Sebastian Bittrich
Scientific Software Developer
RCSB PDB/UCSD
In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website.
On September 22, 2022 a Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.
John Rubinstein (Sick Kid's Hospital, Toronto, Canada)
Macromolecular Machines at Energized Membranes
________________
The 2021 American Crystallographic Association (ACA) Transactions Symposium (July 30-31, 2021) was dedicated to celebrating the manifold contributions of the PDB to fundamental biology, biomedicine, bioenergy, and bioengineering/biotechnology.
Presentations from high profile experimental and computational structural biologists working in the United States, Canada, and South America were augmented by short round table discussions regarding future directions in structural biology and the important role that the Protein Data Bank can play in a rapidly changing landscape.
Access all presentations from this meeting at rcsb.org (https://www.rcsb.org/pages/pdb50-meet..., or use this playlist for chronological recording of the full meeting including panel discussions and introductions (https://www.youtube.com/playlist?list...)
Learn more about neuronal signaling from PDB-101:
Opioids and Pain Signaling: youtube.com/watch?v=ZmrDWIeX0Tc
Neuronal Signaling and Sodium-Potassium Pump: youtube.com/watch?v=ZKE8qK9UCrU
PDB-101 resources on Cellular Signaling: pdb101.rcsb.org/browse/cellular-signaling
This tutorial consists of 2 parts: a brief introduction to the DNA structure and a step-by-step tutorial on how to fold the PDB-101 paper template.
Video Guide:
0:00 Introduction to DNA
1:22 Choosing the template
1:51 Step 1
1:57 Step 2
2:23 Step 3
2:51 Step 4
3:15 Step 5
3:58 Step 6
4:24 Step 7
4:42 Step 8 (optional)
Este tutorial consta de 2 partes: una breve introducción a la estructura del ADN y un tutorial sobre cómo plegar la plantilla de papel PDB-101.
Guía de vídeo:
0:00 Introducción al ADN
1:22 Elegir la plantilla
1:51 Paso 1
1:57 Paso 2
2:23 Paso 3
2:51 Paso 4
3:15 Paso 5
3:58 Paso 6
4:24 Paso 7
4:42 Paso 8 (opcional)
By Isabella Hakim, Kendall Archer, Olivia Spielman, Noah Um
Riverdale Country School, Bronx, NY
Team Advisor: Mrs. Monica Murakami
By Jeslyn Choudhruy, He Xuan, Chloe Zhang
Jericho High School, NY
Team Advisor: Mrs. Serena McCalla
By Xinyi Zhang
South Brunswick High School, NJ
Team Advisor: Mrs. Dana Armstrong