Comparison of RNA 3D Structures

Introduction

Examples

Benchmark

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References

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Query structure

  • Users can choose query structures from the PDB without having to upload their own structure files.

  • The input can be just the 4 letter PDB code, in which case the whole structure corresponding to that PDB entry will be considered. Should you want to specify chains and fragments use the following format -
    • 2vpl

      • The whole structure 2vpl

    • 2vpl,B

      • The structure 2vpl, chain B

    • 2vpl,B,D

      • The structure 2vpl, chains B and D

    • 2vpl,B(2:17),B(29:49)

      • The query in this case would be a 2 fragment structure constituting residues 2-17 and 29-49 of the structure 2vpl, chain B.
  • Rclick allows users to input RNA structures in mmCIF format. The input is the 4 letter PDB code and selected chains. For RNA structures in the mmCIF format, users should specify at least one chain. For example:

    • Note:

    The user uploaded structures cannot be fragments like the chosen PDB structures. The user uploaded structures should be pre-fragmented (if so desired).

    Choice of representative atom

  • A representative atom should be specified exaclty as it appears in the PDB files (upper case, etc).

  • At the least, 3 representative atoms should be present in both structures to be aligned.



    • Root Mean Square Deviation

    Given two RNA structures A and B, root mean square deviation (RMSD) is the norm of the distance vector between the two sets of coordinates of representative atoms, after superimposition. It is given by
    Where, N is the match size, and xiA and xiB are the Cartesian coordinates of representative atoms of structurally equivalent residues of structures A and B.

    Structure Overlap

    Structure overlap (also called equivalent positions) is defined as the percentage of the representative atoms (C3' for RNA structures, and C3' and Cα for RNA-protein complexes) in the structure A that are within 4Å (RMSD cut-off) of the corresponding atoms in the superimposed structure B.

    Match Size

    Match size (also called absolute similarity) is defined as the number of atoms in the list of equivalence.

    Heutistics in structure alignments

    Heurisitics are applied to ensure local chain connectivity. Chain connectivity is broken when equivalent residues are not contiguous in sequence. The equivalent residue matches before the application of heuristics is shown in the output file linked to "Matched residue pairs".

    Rules:

  • Matched segments must have a minimum length of 3 residues (gap matching not included).
      • Residue matches that do not follow this criteria are removed

  • Adjacent segments separated by 3 or less residues are joined together.



    • Fragment Score

    On applying heuristic measures to maintain chain or fragment continuity, some residue matches are eliminated from consideration, as they do not belong to (or are in the close proximity of) contiguously matched fragments. The fragment score is the ratio of the number of matched positions in the alignment before and after the application of heuristics. This is a handy measure to estimate the extent of similarity between two structures. The fragment score is close to 1 (the maximum value) for similar structures.

    Topology Score

    The topology score is a measure of how similar the topologies of the matched structures are to one another. It is computed based on the directionality of the matched sequence fragments. Topology score varies between a maximum of 1 for topologically identical structures and 0 for those are the topologically completely dissimilar.

    In each of the 4 examples, the two structures that are matched consist of 3 different sequence segments. The direction of the arrows that symbolize each segment show the direction from N to C termini. Unless explicitly indicated with black arrows, the segments in the top structure is aligned to one that it is directly above. 4 different cases of sequence alignments implied by Rclick structural alignment are illustrated here a) The sequence alignment maintain topology; topology score = 1. b) The directionality from N To C of the sequence on top is the exact opposite of that to the one in the bottom; topology score = 0. c) Two of the three sequence segments have the same directionality; topology score = 0.66. d) Two of the 3 segments are matched but not in sequential order; topology score = 0.66