# WebFR3D Help

## WebFR3D Help

This document contains information about search options implemented in WebFR3D. Most of this text is also available through contextual help system on the symbolic and geometric search pages. This tutorial describes how to set up WebFR3D searches. If you can’t find an answer to your question, please contact us.

### Synopsis

This diagram summarizes most of the available search options that can be entered in the Query Specification Matrix on the search webpages. Detailed descriptions can be found in the text below.

### Sequential distance constraints

Set limits on the difference between nucleotide numbers using the boxes below the diagonal.  (Actually, what is used is the difference between the index of nucleotides in the file, not NDB nucleotide number.)

• To put an upper limit on the difference, type something like `<5` or `<=5`.

• To put a lower limit on the difference, type something like `>5` or `>=5`.

• To put both limits at once, type something like `>5 <=12`.

• To insist that the nucleotide in the given row have a lower nucleotide number than the nucleotide in the given column, type `<`, separated by a space from other specifications.  For greater, type `>`.

### Interaction constraints

Basepair, base stacking, base phosphate, or letter pair constraint is specified above the diagonal. To specify that all candidate motifs must have a tWH basepair between the nucleotides corresponding to the first and second nucleotides in the query motif, type tWH in the first row, second column. This means that the nucleotide in the first row must use its Watson-Crick edge,  and the nucleotide in the second column must use its Hoogsteen edge.

Valid basepair specifications are: `cWW, tWW, cWH, cHW, tWH, tHW, cWS, cSW, tWS, tSW, cHH, tHH, cHS, cSH, tHS, tSH, cSS, tSS`. Note, however, that the cSS and tSS interactions are not, in fact, symmetric, because each base can use the sugar edge differently. Following Leontis, Stombaugh, Westhof (NAR 2002), type `cSs` to specify that the first base has priority, `csS` for the second, or `cSS` for either.

Specifying multiple interactions allows more ways a candidate can satisfy the constraints; for example, typing `cWH cHW` requires a cis Watson-Crick/Hoogsteen basepair, but either base can use the Watson-Crick edge, and the other uses the Hoogsteen edge.

The abbreviation `trans` gives all trans categories, `cis` for cis.

Type `bif` for bifurcated basepairs (see NAR 2002).

Type `~cWW` to exclude candidates having a cWW basepair.

Some pairs of bases are close to, say, cWW, but do not meet the strict criteria for membership in the cWW classification. Type `ncWW` (“near cWW”) to get basepairs that are  not classified into any category, but for which the cWW category is the closest match, up to a certain fairly generous limit. Type `cWW ncWW` to get cWW and near cWW pairs, cWW. Type `ntrans` to get all pairs nearest to a trans pair.

Type `s35` for stacking in which the first base uses its 3 face, and the second base uses its 5 face. Similarly, type `s53`, `s33`, or `s55`. Type `stack` to allow all stacking interactions. The prefixes “n” and “~” work with stacking, as above.

To specify that the nucleotides must match a certain pattern, type, for example, `cWW CG GC` to get only CG or GC cWW pairs.

To require that two nucleotides make a base-phosphate interaction, enter `BPh` in the corresponding yellow box. This will select pairs of nucleotides in which the first nucleotide’s base is a hydrogen bond donor and the second nucleotide’s phosphate is an acceptor. To reverse the roles, type PhB. To specify particular base-phosphate categories, type `0BPh, 1BPh, 2BPh, ..., 9BPh, or 0PhB, 1PhB`, etc. For near base-phosphate interactions, type `nBPh, nPhB, n1BPh, n1PhB`, etc. See the original paper about classification of base-phosphate interactions for more information.

One can restrict to pairs that play a certain role in the secondary and tertiary structure.  For pairs that are nested, type N” or `nested`.  For pairs that cross nested interactions but involve nucleotides in the same branch of the RNA, type `local` or “L”.  For long-range or distant interactions, between different branches of the RNA, type `long-range`, `distant`, “D”, or “LR”.  Note that “nested”, “local”, and “distant” are mutually exclusive.  They can be negated with ~, but ~local only returns distant interactions, not nested ones.

To find bases which are in the same plane and are close enough that they may hydrogen bond in some way, type `coplanar` or `cp`.  Near and not coplanar can be obtained with the "n" and "~" prefixes, respectively.

To specify bases that participate in cWW pairs and that delimit a single-stranded region such as a hairpin loop or one strand in an internal or junction loop, type "`flankss" or "flank" or "F"`. Note: for internal and junction loops, flanking nucleotides will be on the same strand, one on each side of the loop. Such flanking nucleotides usually do not interact with one another.  In a hairpin, however, the nucleotides in the closing basepair simultaneously make a cWW pair and satisfy the flankss relation.

### Nucleotide identity constraints

The user can impose a nucleotide identify constraint (nucleotide mask) for their search by putting in nucleotide constraints in the text-boxes on the diagonal in the Interaction Matrix, which has a white background. Typing `A`, for instance, means that only candidate motifs with an A in the corresponding position will be kept. Typing `AG` allows either A or G, etc.

The program uses these standard abbreviations for other combinations:

• M for A or C
• R for A or G
• W for A or U
• S for C or G
• Y for C or U
• K for G or U
• V for A, C, or G
• H for A, C, or U
• D for A, G, or U
• B for C, G, or U
• N for A, C, G, or U

Note that N is the default. One may also exclude a given base using the syntax `~G`

for instance, to exclude candidates with a G in the corresponding position.

### Nucleotide numbers

Nucleotides must be separated by commas, you can specify ranges using colons.

You can insert any number of spaces. The ordering of nucleotides doesn't matter.

These examples are equivalent:

• 1856:1860, 1882:1886
• 1860:1856, 1886:1882
• 1856,1857:1859,1860,1882:1884,1885,1886
• 1856,1857,1858,1859,1860,1882,1883,1884,1885,1886

### RNA-containing PDB files

The list of PDB files is updated weekly (on Saturdays) to include all available RNA-containing PDB files. If you do not see a file, please let us know about it using the contact form. WebFR3D also includes several non-redundant lists of PDB files at various resolutions. More information about the non-redundant lists can be found on the non-redundant lists website and in the NAR 2009 paper. In the next updates of WebFR3D, these lists will be automatically updated on a weekly basis.

### Discrepancy

Geometric discrepancy is a measure of how similar RNA structures are. Higher geometric discrepancy corresponds to more dissimilar structures. Identical structures have discrepancy zero. Searches with high geometric discrepancy cutoffs take significantly longer than those with lower cutoffs.

Geometric discrepancy is an entirely geometric measure that takes into account the general shape of the candidate motif and the orientations of its bases. First, we determine the shift vector and rotation matrix which map the geometric centers of the bases of each candidate motif onto the corresponding base centers in the query motif with the smallest error, called the fitting error. After the rigid body operations are performed, we compute the angles of rotation needed to align each base of the candidate with the corresponding base of the query motif. The square root of the sum of the squares (RMS sum) of these angles (in radians) is called the orientation error. The geometric discrepancy is defined to be the RMS sum of the fitting and orientation errors, divided by the number of bases in the query motif.

For more information about geometric discrepancy, please see the original FR3D paper.

### Email

You can optionally specify your email to receive a notification once your search has completed.