CoSSMos Database Frequently Asked Questions

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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]


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

An example of the C2' endo conformation. The C2' atom is on the same side of the ring's plane as the C5' atom. [2]
An example of the C2' exo conformation. The C2' atom is on the opposite side of the ring's plane as the C5' atom. [3]
An illustration of A. an anti glycosidic linkage and B. a syn glycosidic linkage.[4].
A. A purine with the three edges labeled. B. A pyrimidine with the three edges labeled. In RNA CoSSMos nomenclature, the C-H Edge is equivalent to the Hoogsteen edge. [5]

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.

How do I use the tabulated results for NMR structures?

When NMR is used to solve a structure, multiple structures are solved to form an ensemble. In order to more efficiently compare these structures, we have compiled them into the table. The first structure in the ensemble is arbitrarily designated as 'prime' and the rest are compared to that structure. If the data matches, it is colored green, but if the data is different, for example anti instead of syn, the text is in red. A quick glance across the page will show if the ensemble has any discrepancies between the structures.

Table 1. Symbols and definitions of Interacting Edge Nomenclature[10]
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 keep getting an error message when I try to view the clipped structure. What should I do?

You need to have Java installed on your computer in order to view the three-dimensional clipped structure. In order to do this, please visit the Java homepage [4] and follow the instructions found there. If you have successfully installed JAVA, and still cannot view the clipped structure, please contact us at cossmos@slu.edu.

Download Results

My downloaded results are not in columns. How do I change this?

The RNA CoSSMos downloadable results downloads as a pound-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. Click Other and type in #. 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.

Table 2. Abbreviated column headings and definitions
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)
A Closing Base Pair The sugar pucker and glycosidic linkage for the closing base pair nucleotides on the "top" strand
B Closing Base Pair 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
Closing Base Pair Closing Base Pair ie 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
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


References

  1. 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.
  2. Bloomfield, V.A., Crothers, D.M., et al. (2000). Nucleic Acids: Structures, Properties, and Functions. Salsaltio, CA, University Science Books.
  3. Bloomfield, V.A., Crothers, D.M., et al. (2000). Nucleic Acids: Structures, Properties, and Functions. Salsaltio, CA, University Science Books.
  4. Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
  5. Leontis, N.B., Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs, RNA. 7:499-512.
  6. Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
  7. Saenger, W. (1984). Principles of Nucleic Acid Structure. New York, Spring-Verlag.
  8. Leontis, N.B., Westhof, E. (1998). Conserved geometrical base-pairing patterns in RNA, Quaterly Review of Biophysics. 31(4):399-455.
  9. Leontis, N.B., Westhof, E. (2001). Geometric nomenclature and classification of RNA base pairs, RNA. 7:499-512.
  10. Laboratoire de Biologie Informatique et Th´eorique. (2004). MC-Sym 3.3.2 User Manual