SNAP revision history

[xiangjun]

As the list is becoming quite long, for easy reference, I have split up the DSSR release notes from the main post "SNAP: software for characterizing DNA-protein interactions".

SNAP has been integrated into DSSR, and is available from the Columbia Technology Ventures (CTV) website.

Release history (in reverse chronological order):

• v1.0.7-2020sep09 -- miscellaneous code refinements.
• v1.0.6-2019sep30 -- Added the --methyl-C option dedicated to the characterization of interactions between DNA 5-methyl cytosine (5CM) and amino acids in DNA-protein complexes.
• v1.0.5-2019sep16 -- Documented variations on the --get-hbond option.
• v1.0.4-2019aug26 -- Added the --json option for easy parsing of SNAP output; Expanded base-pair/amino-acid interactions to include all base pairs listed in the helices section; plus miscellaneous code refactoring and refinements.
• v1.0.3-2019aug03 -- Added a list of modified nucleotides (such as 5CM) to the main output as in DSSR; Fixed a bug in rare cases, plus miscellaneous code refinements.
• v1.0.2-2019mar28 -- Revised the algorithm for the identification of stacking interactions between planar side-chains of amino acids with bases of DNA/RNA.
• v1.0.1-2019feb11 -- Along with DSSR, refined code and fixed a couple of bugs in rare occasions.
• v1.0.0-2019feb03 -- After four years of continuous developments based on my own research and users' feedback, SNAP is mature and robust enough to merit the version 1.0 release. SNAP shares the codebase and follows the same style as DSSR, and it aims to become a preferred software tool for the analyses of DNA-protein or RNA-protein 3D structures.

• beta-r16-2018sep06 -- added the --citation option; numerous code refinements along with DSSR.
• beta-r15-2018feb15 -- added a new section that lists interface stack(s) with 3+ planar moieties. An interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default).
• beta-r14-2018jan05 -- added the --nmr option; classified H-bonds into six categories: phosphate/sugar/base moieties for nucleotides vs backbone/sidechain for amino acids.
• beta-r13-2017dec31 -- simplified output of H-bonds into mutually exclusive sections (phosphate group, sugar, or base with amino acid); added option --auxfile for producing additional auxiliary files (the default is now only the main output file); miscellaneous bug fixed and code refinements.
• beta-r12-2017dec26 -- added a summary section of nucleotides with interacting amino acids; revised code to avoid warning messages with GCC v7.
• beta-r11-2017dec11 -- revised output wording/formatting; added a list of additional files for pairwise H-bonding, base-amino acid pairing/stacking interactions; plus numerous code refinements.
• beta-r10-2017apr10 -- documented the --type=string where string can be "base" (the default), "backbone", "either", or "both". The "base" argument reports protein interactions with only DNA/RNA base atoms, "backbone" with only DNA/RNA backbone atoms, "either" with base or backbone atoms, and "both" with base plus backbone atoms.
• beta-r09-2016sept28 -- fixed a bug with the --cleanup option (thanks to jms89).
• beta-r08-2016jun02 -- added the --tshape (or --t-shape) option to fix issues reported in the Supplemental Table S1 of the Wilson et al. paper "Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts". Specifically, the authors said:
  
  "Furthermore, although the recently released beta-r06-2015oct23 version of 3DNA-SNAP (Lu and Olson 2008) is able to distinguish between such errors, and accurately detects stacking interactions between nucleobases and amino acids, it unfortunately is currently unable to identify T-shaped interactions (see, for example, Supplemental Table S1)."
  
  
• beta-r07-2016may21 -- fixed the "Segmentation fault" bug (due to undefined reference frames for certain amino acids with missing side-chain atoms); miscellaneous internal code refinements.
• beta-r06-2015oct23 -- detected aromatic stacking interactions between bases and amino acids; numerous refinements along with DSSR.
• beta-r05-2015may03 -- added option --get-hbond to output a list of H-bonds between protein and nucleic acid; numerous internal code refinements.
• beta-r04-2014sep30 -- removed the (undocumented) --rna option so that RNA-protein complexes are handled the same way as DNA-protein complexes; relaxed default settings so SNAP now runs on pure nucleic acid or protein structures in addition to their complexes; added DSSP output for the protein component in file snap-dssp.txt.
• beta-r03-2014sep16 -- listed base-AA pseudo-pairs and output an associated PDB ensemble file (snap-pseudoPairs.pdb); significant code speed-up.
• beta-r02-2014may31 -- detailed listing of H-bonding interactions between a component of nucleotide (base/phosphate/sugar) and an amino acid.
• beta-r01-2014may05 -- initial release to kick the ball rolling. SNAP identifies base-AA or BP-AA interactions based on a distance cutoff (default to 4.5 angstrom), calculates six parameters to uniquely quantify the spatial relationships, and sets the coordinates in the standard base or BP reference frame for easy visualization and for deriving knowledge-based potentials.