Difference between revisions of "BIN-PDB"
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | <!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" --> | ||
You need to complete the following units before beginning this one: | You need to complete the following units before beginning this one: | ||
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*[[BIN-SX-Concepts]] | *[[BIN-SX-Concepts]] | ||
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== Contents == | == Contents == | ||
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| + | |||
| + | {{Task|1= | ||
| + | *Read the introductory notes on {{ABC-PDF|BIN-PDB|the Protein DataBase (PDB) - the global data repository for protein 3D structure information}}. | ||
| + | }} | ||
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| + | ==The PDB== | ||
| + | ; Search for GO and EC numbers at PDB... | ||
| + | |||
| + | The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started. | ||
| + | |||
| + | |||
| + | {{task| | ||
| + | # Visit the RCSB PDB website at http://www.pdb.org/ | ||
| + | # Briefly orient yourself regarding the database contents and its information offerings and services. | ||
| + | # Enter <code>Mbp1</code> into the search field. | ||
| + | # In your journal, note down the PDB IDs for the three ''Saccharomyces cerevisiae'' Mbp1 transcription factor structures your search has retrieved. | ||
| + | # Click on one of the entries and explore the information and services linked from that page. | ||
| + | }} | ||
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== Further reading, links and resources == | == Further reading, links and resources == | ||
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| − | + | * [http://www.wwpdb.org/documentation/format23/v2.3.html '''PDB file format'''] | |
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Revision as of 04:27, 31 August 2017
The RCSB-PDB Structure Database
Keywords: The RCSB PDB database and services
Contents
This unit is under development. There is some contents here but it is incomplete and/or may change significantly: links may lead to nowhere, the contents is likely going to be rearranged, and objectives, deliverables etc. may be incomplete or missing. Do not work with this material until it is updated to "live" status.
Abstract
...
This unit ...
Prerequisites
You need to complete the following units before beginning this one:
Objectives
...
Outcomes
...
Deliverables
- Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
- Journal: Document your progress in your course journal.
- Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.
Evaluation
Evaluation: NA
- This unit is not evaluated for course marks.
Contents
Task:
- Read the introductory notes on the Protein DataBase (PDB) - the global data repository for protein 3D structure information.
The PDB
- Search for GO and EC numbers at PDB...
The search options in the PDB structure database are as sophisticated as those at the NCBI. For now, we will try a simple keyword search to get us started.
Task:
- Visit the RCSB PDB website at http://www.pdb.org/
- Briefly orient yourself regarding the database contents and its information offerings and services.
- Enter
Mbp1into the search field. - In your journal, note down the PDB IDs for the three Saccharomyces cerevisiae Mbp1 transcription factor structures your search has retrieved.
- Click on one of the entries and explore the information and services linked from that page.
Further reading, links and resources
Notes
Self-evaluation
If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
About ...
Author:
- Boris Steipe <boris.steipe@utoronto.ca>
Created:
- 2017-08-05
Modified:
- 2017-08-05
Version:
- 0.1
Version history:
- 0.1 First stub
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
