CoSSMos Database Frequently Asked Questions
Welcome to the Znosko Lab RNA CoSSMos [1] Frequently Asked Questions.
The RNA CoSSMos Database was created by the Znosko and Kirkpatrick Labs at Saint Louis University to give researchers the ability to easily search through the nucleic acid structures from the Protein Data Bank [2][1] and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. We have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type.
Below are some of the most common questions, sorted by the website pages. If your question does not appear here, please contact us. [3]
Contents
General Questions
How do I register with the CoSSMos Database?
We recommend registering with the database before you begin to use it. To register, go to the Log-In page. There, you will see a link that will allow you to quickly register. You will be asked for a username, a password, and information about your place of employment. This is to better help us understand the needs of the users of the CoSSMos Database.
How do I change my user profile?
If you are a registered user, on the top left corner of the page, you will see a link called Control Panel. When you click this link, it will take you to a page where you are able to change your password and your email address.
I am a developer working in academia or industry and I wish to use your database data directly in my program. How may I go about doing so?
RNA CoSSMos has an API specially developed for developers to facilitate the direct access of database information by allowing queries to be passed through an HTTP interface. Information regarding the API, including general use and syntax, may be found at the RNA CoSSMos API FAQ page.
Search Page
How does the Nucleic Acid Sequence Search work?
For double stranded mismatches, you will use both the 5'-3' and the 3'-5' boxes. For a hairpin loop, you will only need to use the 5'-3' box. The closing base pairs can be chosen from the drop-down menus of the smaller boxes on either side; they are labeled Opening and Closing Nucleotides. The mismatch sequence that you are looking for can be entered into the middle, longer boxes.
What if I'm looking for a general type of mismatch, like a purine-purine mismatch?
The sequence search can recognize the nucleotides A, U, C, and G. The search can also recognize R for A and G, Y for U and C, or N for all nucleotides. Any of these can be entered into the sequence search to give all possible combinations.
What sort of keywords can I use to search through the database?
Keywords that this database uses come from the keywords and headers that the PDB files themselves use. Some common keywords are ribosome, capsid, ribozyme, and riboswitch. However, if you are not sure for exactly what you are looking, we recommend leaving this field blank.
I want to keep the results from this search for future reference. How can I do this?
The CoSSMos Database can save up to 10 searches when registered users are logged in. To do this, simply click the box at the bottom of the search page. This will then prompt you to enter a search name, up to 256 characters. In the future, if these results are no longer needed, click the X beside the search's name.
Refined Search and Subqueries
When I click on Refine Search, a pop-up shows and asks me if I want to refine the search parameters or search within these results. What is the difference?
When you need to refine your search, there are two possible options. The first is to simply change the parameters that you have already searched, including general information, experimental parameters, motifs, and sequence. The second option will bring you to our subquery page. This allows the user to search within the results, but specify structural information, including sugar pucker, glycosidic bond, base pairing, and stacking interactions.
How does the subquery search work?
After completing the initial search on the standard COSSMos queries, you have the option of searching via specific structural characterizations. Simply select which interaction you wish to specify, use the drop-down menu to choose the possible interactions, and click Add Parameter. A link to the results of the new search will appear on the bottom of the page, under the Query Builder.
Detailed Results
What does it mean when it says "sugar pucker and glycosidic conformation?"
This refers to the pucker of the mismatched bases's ribose or deoxyribose and to the sugar-base bond orientation. With all glycosidic conformations listed, the first term is the carbon atom of the sugar that is puckered. The second term is the type of pucker of the sugar, either endo or exo, depending on if the major pucker is on the same side (endo) of C5' or on the opposite (exo); the third term is the conformation of the sugar-base bond, either syn or anti[6].
What do the numerals mean under "Interacting Edges?"
This database uses both Saenger's[7] and Westhof's[8] notation, which is found as either a Roman or Arabic numeral within the parentheses. The numbers correspond to a specific conformation of the two bases that are involved in the base pairing.
What do the letters mean in "Interacting Edges?"
The letters show which region of the base is actually participating in hydrogen bonding. Nitrogenous bases have three sides: the Watson-Crick edge (W), the Hoogsteen edge (H), and the Sugar edge (S). The figure below shows the three different edges of the purine and the pyrimidine bases [9]. In the notation on the Detailed Results page, the capital letter designates which edge is involved, while the lowercase letter designates which part of the edge is involved. In the table below, every combination of capital and lowercase letters can be found, along with a description of the region involved with the hydrogen bonding.
| Symbol | Definition |
|---|---|
| any | Any of the residue faces involved |
| W | Watson-Crick face involved |
| Ww | Center of the Watson-Crick face involved |
| Wh | Watson-Crick face involved, near the Hoogsteen face |
| Ws | Watson-Crick face involved, near the Sugar face |
| H | Hoogsteen face involved |
| Hh | Center of the Hoogsteen face involved |
| Hw | Hoogsteen face involved, near the Watson-Crick face |
| C8 | Hoogsteen face involved, near the C8 atom |
| S | Sugar face involved |
| Sw | Sugar face involved, near the Watson-Crick face |
| Ss | Center of the Sugar face involved |
| B | Bifurcated face involved |
| Bs | Bifurcated face involved, near the Sugar face |
| Bh | Bifurcated face involved, near the Hoogsteen face |
I see a black box for the structure viewers. What should I do?
If you are using:
- Internet Explorer: Sorry, Internet Explorer doesn't support WebGL.
- Firefox (version 4 or later): try force enabling WebGL[4].
- Google Chrome: try force enabling WebGL [5].
- Safari: enable WebGL [6].
How are the clipped PDB files named?
The clipped PDB files are named with the PDB ID, top strand sequence (5'-3') and bottom strand sequence (3'-5'), the chain and residue number of the first residue in the loop, and the model number followed by the .pdb extension.
Download Results
My downloaded results are not in columns. How do I change this?
The RNA CoSSMos downloadable results downloads as a tab-delimited file. To put this in columns in Excel, highlight column A and click on the Data tab. Then click on Text to Columns button. Once the window opens, select "Delimited" and click Next. In this window, the "Tab" will already be marked as a delimiter. Once you hit finish, the data will be in columns.
What do the column headings mean in the downloaded results?
Below is a table with the column headings and an explanation of each.
| Column Headings | Signification |
|---|---|
| pdb | PDB ID Number |
| Aseq | The sequence for the "top" strand |
| Bseq | The sequence for the "bottom" strand |
| Aseq_num | The nucleotide numbers for the "top" strand |
| Bseq_num | The nucleotide numbers for the "bottom' strand |
| A Residue Conformation | The sugar pucker and glycosidic linkage for the mismatched/bulged nucleotide(s) on the "top" strand |
| B Residue Conformation | The sugar pucker and glycosidic linkage for the mismatched/bulged nucleotide(s) on the "bottom" strand |
| Loop Interacting Edges | Any hydrogen bonding interactions between mismatched/bulged nucleotide(s) |
| Acbp | The sugar pucker and glycosidic linkage for the closing base pair nucleotides on the "top" strand |
| Bcbp | The sugar pucker and glycosidic linkage for the closing base pair nucleotides on the "bottom" strand |
| 5' Closing Base Pair Interacting Edges | Any hydrogen bonding interactions between the 5' closing base pair nucleotides |
| 3' Closing Base Pair Interacting Edges | Any hydrogen bonding interactions between the 3' closing base pair nucleotides |
| cbpcbpie | Any hydrogen bonding interactions between the 5' and 3' closing base pairs |
| Loop Closing Base Pair Interaction | Any hydrogen bonding interactions between the mismatched/bulged nucleotide and either closing base pair |
| Adjacent Stacking | Any stacking interactions between neighboring nucleotides within the motif |
| Non-adjacent Stacking | Any stacking interactions between non-neighboring nucleotides within the motif |
| stacks | Total number of stacking interactions in the motif |
| Adjacent Stackings | Total number of adjacent stacking interactions in the motif |
| Non-adjacent Stackings | Total number of non-adjacent stacking interactions in the motif |
| header | The header found on the PDB.txt file |
| date | The date that the PDB file was published |
| title | The title of the accompanying article that solved the PDB structure |
| experiment | The experimental method that was used to solve the structure |
| resolution | The resolution of the X-Ray diffraction or Cryo-Electron Microscopy experiment |
| model | The model number in the PDB file. An asterisk denotes an NMR representative structure. |
| structures | The number of Structures in an NMR ensemble |
| author | The authors of the journal article |
| reference | The reference of the journal article |
| keywords | Any keywords that are found in the PDB text file |
| creationdate | The date the PDB structure was deposited into the RNA CoSSMos Database |
Average Structure
Why do I only see three atoms for each base in the average structure?
To allow users to calculate average structures from structures with different sequences, the average structure is calculated using all of the backbone atoms and only three atoms from each base (N9, C8, and C4 for A or G) (N1, C2, and C6 for U or C).
Why do I get a warning for the average structure?
When calculating the average structure of the structures that you selected, an RMSD is calculated between the first structure and all of the other structures. If the RMSD is greater than 1.0 Å, the average structure angles and bond lengths may not be realistic and therefore the structure may not be physically meaningful.
Results Summary
How are the motifs numbered?
For hairpin loops, the 5’ closing base is assigned as the first base, with the remaining bases assigned sequentially from the 5’ to the 3’ end. For internal and bulge loops, the 5’ closing base of the “A” strand or “top” strand is assigned as the first base, with the remaining bases in this strand assigned sequentially from the 5’ to the 3’ end. The 5’ closing base of the “B” strand or “bottom” strand is assigned the next position where the “A” strand left off, then the remaining bases in the “B” strand are sequentially assigned from the 5’ to 3’ end.
What are the Combinations tables?
The "Sugar Pucker & Glycosidic Conformation" tables report the percentages of the different combinations of sugar puckers with glycosidic conformations for each residue within your dataset. There are two of these tables--one for the motif structure and a second for the closing base pair structure. The "Conformations and Interacting Edges" tables are a collection of tables that report the percentages of the different detailed interaction types between two residues with the corresponding combined sugar pucker and glycosidic conformations. A separate table is calculated for each pair of interacting residues. The "Stacking and Conformations" tables are a collection of tables that report the percentages of the different detailed stacking types between two residues with the corresponding combined sugar pucker and glycosidic conformations. Similar to the "Conformations and Interacting Edges" tables, a separate table is calculated for each pair of stacking residues for the "Stacking and Conformations" tables. The "Combined Conformations and Interacting Edges" table reports the percentages of the different combinations of ALL detailed interacting edges and ALL combined sugar pucker and glycosidic conformations. Likewise, the "Combined Conformations and Stacking" table reports the percentages of the different combinations of ALL detailed stacking interactions and ALL combined sugar pucker and glycosidic conformations. These last two tables become very large if you have a lot of variation in structure within your dataset. If web-viewing becomes difficult, it is recommended that you download the table and view it in Excel.
What are all of the files in the downloaded zipped archive?
Each table on the Results Summary page is saved as a tab-delimited text file.
| Results Summary Table | Download Filename |
|---|---|
| Motif Structure | |
| Sugar Pucker | motifstructure_sugarpucker.txt |
| Glycosidic Conformation | motifstructure_glycosidicconformation.txt |
| Interacting Edges | motifstructure_interactingedge.txt |
| Interacting Edges (Detailed) | motifstructure_interactingedgedetailed.txt |
| Closing Base Pair Structure | |
| Sugar Pucker | closingbp_sugarpucker.txt |
| Glycosidic Conformation | closingbp_glycosidicconformation.txt |
| Interacting Edges | closingbp_interactingedge.txt |
| Interacting Edges (Detailed) | closingbp_interactingedgedetailed.txt |
| Other Interactions | |
| Interacting Edges | other_interactingedge.txt |
| Interacting Edges (Detailed) | other_interactingedgedetailed.txt |
| Stacking Interactions | |
| Adjacent Stacking | other_adstack.txt |
| Adjacent Stacking (Detailed) | other_adstackdetailed.txt |
| Non-Adjacent Stacking | other_nonadstack.txt |
| Non-Adjacent Stacking (Detailed) | other_nonadstackdetailed.txt |
| Combinations | |
| Motif Structure Sugar Pucker & Glycosidic Conformation | motifstructure_puckerandglycosidic.txt |
| Closing Base Pair Sugar Pucker & Glycosidic Conformation | closingbp_puckerandglycosidic.txt |
| Conformations and Interacting Edges | comboInteracing_Edge_#-#.txt, where #s are the residues involved in the interaction |
| Stacking and Conformations | comboStacking_#-#.txt, where #s are the residues involved in the stack |
| Combined Conformations and Interacting Edges | combointeractions.txt |
| Combined Conformations and Stacking | combostacks.txt |
References
- ↑ Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
- ↑ Bloomfield, V.A., Crothers, D.M., et al. (2000). Nucleic Acids: Structures, Properties, and Functions. Salsaltio, CA, University Science Books.
- ↑ Bloomfield, V.A., Crothers, D.M., et al. (2000). Nucleic Acids: Structures, Properties, and Functions. Salsaltio, CA, University Science Books.
- ↑ Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
- ↑ Leontis, N.B., Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs, RNA. 7:499-512.
- ↑ Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
- ↑ Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
- ↑ Leontis, N.B., Westhof, E. (1998). Conserved geometrical base-pairing patterns in RNA, Quaterly Review of Biophysics. 31(4):399-455.
- ↑ Leontis, N.B., Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs, RNA. 7:499-512.
- ↑ Laboratoire de Biologie Informatique et Th´eorique. (2004). MC-Sym 3.3.2 User Manual
