What find_pair in 3DNA can do

Structural analysis of nucleic acids used to be a rather tedious process, especially for irregular, complicated RNA structures and nucleic-acid/protein complexes [e.g., the large ribosomal subunit of H. marismortui (1jj2)]. Without valid base-pairing information arranged properly in a duplex fragment as input, analysis programs such as Curves+ and analyze/cehs in 3DNA would produce meaningless results. The program find_pair in 3DNA was originally created to solve this specific problem, i.e., to generate an input file to 3DNA analysis routines directly from a nucleic-acid containing structure in PDB format. It is what makes nucleic acids structural analysis a routine process — running through thousands of structures from NDB/PDB can be fully automated.

Overall, find_pair has more than fulfilled the goal of its initial design (as stated above). Over the past few years, its functionality has been expanded and continuously refined (kaizen 改善), making find_pair itself a full-featured application. Now, it is efficient, robust, and its simple command line interface allows for easy integration with other bioinformatics tools. Properly acknowledged or otherwise, find_pair has served (at least) as one of the key components in many other applications (RNAView, BPS, SwS, ARTS, to name just a few). Indeed, find_pair is by far the single program in 3DNA that has received the most questions (as evident from the 3DNA forum).

While I still have to write a method paper to describe the underlying algorithms of find_pair in detail — i.e., for identifying nucleotides, H-bonds, base pairs, high-order base associations, and double helical regions — the basic idea is intuitive and very easy to understand: as summarized in our recent GpU paper”, find_pair is purely geometric based (with user adjustable parameters) and allows for the identification of canonical Watson–Crick as well as non-canonical base pairs, made up of normal or modified bases, regardless of tautomeric or protonation state. For example, in the GpU paper”, we chose the following set of stringent parameters to ensure that the geometry of each identified base pair is nearly planar and supports at least one inter-base H-bond: (i) a vertical distance (stagger) between base planes ≤ 1.5 Å; (ii) an angle between base normal vectors ≤ 30°; and (iii) a pair of nitrogen and/or oxygen base atoms at a distance ≤ 3.3 Å. Other criteria (documented or otherwise), such as the distance between the origins of the two standard base reference frames, are just filters to speed up the calculations.

In a nutshell, find_pair has the following two core functionalities:

  • The default is to generate input to the analysis routines in 3DNA (analyze/cehs) for double helices. However, there are many more job to perform under the hood than just identifying base pairs: the base pairs must be in proper sequential order, and each strand must be in 5’ to 3’ direction, for the calculated step parameters (twist, roll etc) to make sense. Moreover, with the “-c” option, one gets an input file to Curves (but not Curves+, yet); with the “-s” or “-1” option, find_pair treats the whole structure as one single strand, and is useful for getting all backbone torsion angles.
  • Detect all base pairs (regardless of double helical regions) and higher-oder (3+) base associations with the “-p” option. This feature (in its preliminary form) was there starting from at least v1.5, which was released at the end of 2002 (just before I left Rutgers), but it was intentionally undocumented. The source code of find_pair (as part of 3DNA) was tested and shared within Rutgers (NDB and Dr. Olson’s laboratory) before any 3DNA paper was published, and served as the basis for several other projects. We also offered 3DNA (with source code) to a few RNA experts for comments; but we received either no responses or politely-worded negative ones. Things did not work out as (what I thought) they should have been, but that’s life and I have learned my lessons. The “-p” option was first explicitly mentioned in the 3DNA 2008 Nature Protocols paper, to illustrate how to identify the two pentaplets in the large ribosomal subunit of H. marismortui (1jj2).

It is interesting to mention the two papers I’ve recently come across: the first is on DNA-protein interactions and the second on RNA base-pairing, where new algorithms were developed to detect base pairs and their performances were compared with find_pair. In each of the two cases, it was claimed that find_pair missed certain pairs where the new methods succeeded. As it turned out, however, in the first case, simply relaxing find_pair’s default H-bond distance cut-off 4.0 Å to 4.5 Å, as used by the authors, virtually all the missing pairs were recovered. In the second case, the “-p” option, which should have been, was simply not specified.

After nearly a decade of extensive real-world applications and refinements, it is safe to say that find_pair is now a versatile and practical tool for nucleic acids structure analysis. Of course, I will continue to support and further refine find_pair as I see fit. Once in a while, I just cannot stop but to think that find_pair is to nucleic acids what DSSP is to proteins: simple and elegant. As more people become aware of its existence, I would expect find_pair to gain even more widespread usage, especially in RNA-structure related research areas.

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