ssdl-snu/snupi

SNUPI (Structured NUcleic-acids Programming Interface)

SNUPI

SNUPI is a multiscale analysis framework for the prediction of structured DNA assemblies.

Updates

• v3.10 (2024-07-29)
  • EtBr-binding simulations
• v3.01 (2024-01-24)
  • Minor error fix
• v3.00 (2023-09-27)
  • Dynamic simulations
  • Restarting simulations
  • GPU acceleration
• v2.01 (2022-01-18)
  • Minor error fix
• v2.00 (2021-11-19)
  • Analysis of wireframe or topologically-closed designs
  • export of the oxDNA input file format.
  • Improved modeling of the single-stranded DNA
• v1.01 (2021-02-23)
  • Support for command line execution (see protocol.pdf)
  • Support for mac and linux
  • Minor error fix
• v1.00 (2021-01-07)
  • Initial upload

Prerequisite

• The correct version of the MATLAB Runtime should be installed.
• v3: Runtime version R2022b (9.13)
• v2: Runtime version R2019a (9.6)
• v1: Runtime version R2019a (9.6)
• Download link: http://www.mathworks.com/products/compiler/mcr/index.html

How to run (Window)

• Execute 'SNUPI.exe'
• The example result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

How to run (Linux)

• Open the terminal
• Move the current directory to the SNUPI folder
• Give permission to execute
  • chmod +x *
• Execute SNUPI
  • ./run_SNUPI.sh <mcr_directory>
• For example,
  • ./run_SNUPI.sh /usr/local/MATLAB/MATLAB_Runtime/R2022b
• The result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

How to run (Mac)

• Open the terminal
• Move the current directory to the SNUPI folder
• Give permission to execute
  • chmod +x *
• Execute SNUPI in the FILE folder using Terminal
  • ./run_SNUPI.sh <mcr_directory>
• For example,
  • ./run_SNUPI.sh /Applications/MATLAB/MATLAB_Runtime/R2022b
• The result files will be saved in the 'OUTPUT' folder.
• To analyze custom design files, modify 'Input.txt'

Assign design files

• Modify the 'Input.txt' file to assign design files.
• In the 'Input.txt' file, <lattice_type> and <file_directory> should be denoted.
• Use caDNAno design files (json and csv).
• The percentage mark ('%') represents comments
• Example designs were already assigned.

Technical details

• SNUPI framework (static analysis): Rapid computational analysis of DNA origami assemblies at near-atomic resolution, ACS Nano (2021), https://doi.org/10.1021/acsnano.0c07717
• Improved model of single-stranded DNA: Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies, ACS Nano (2021), https://doi.org/10.1021/acsnano.1c08861
• Partition and relocation framework (free-form structures): Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint, ACS Nano (2022), https://doi.org/10.1021/acsnano.1c10347
• Langevin dynamics simulations: A computational model for structural dynamics and reconfiguration of DNA assemblies, Nature Communications (2023), https://doi.org/10.1038/s41467-023-42873-4
• Graph neural network (Deep SNUPI): Prediction of DNA origami shape using graph neural network, Nature Materials (2024), https://doi.org/10.1038/s41563-024-01846-8
• EtBr-binding simulations: Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2023), https://doi.org/10.1038/s41467-024-50871-3

snupi's Issues

Design error

I am able to use the example .json files, but when I run my file I get the following error

!! Design error
!!Please check lattice-type (honeycomb or square)
!! Or, please not locate bp-deletion on crossovers

I'm not sure what this means because I know I picked the right lattice type, I don't know how to fix the latter.

MAC v3_00 Error: Cannot find CTF archive

Hi,

I would love to try out the new v3_00 version on my Mac. However in my first test trying to run an example, I received an error: "Error: Cannot find CTF archive"
version SNUPI_v2_01_mac works without problems.

Test in the input file is:
H EXAMPLE/Ex4_Triangle_dynamic

terminal input:

sh ./run_SNUPI.sh /Applications/MATLAB/MATLAB_Runtime/R2022b

terminal output:

------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/MATLAB/MATLAB_Runtime/R2022b/runtime/maci64:/Applications/MATLAB/MATLAB_Runtime/R2022b/bin/maci64:/Applications/MATLAB/MATLAB_Runtime/R2022b/sys/os/maci64
Error: Cannot find CTF archive '/Applications/SNUPI_v3_00_mac/SNUPI.app/Contents/Resources/SNUPI_mcr/.META/manifest.xml'. 

Browsing through the directories, the .META folder indeed does not exist. Please let me know if you require further information. Thanks for your help.

Best,
Fabian

Inconsistency between the design files and the oxDNA output.

When I'm running the example triangle structure 4 asking for the oxDNA output the resulting structure is missing the single stranded regions specified in the example design file.
Have tried to run this on SNUPI3, setting the following input file option.
STT_FINL_OX 1
Am not sure if other versions are affected.

Import Sequences

I get the same error when I upload the exported sequence .csv from cadnano alongside my .json file. I tested and found that the .json file works fine, but once I upload the .csv file it won't run. Here are the two files I'm trying to run as well as the error I get

Error using get_CSV_SEQ (line 10)
Assertion failed

Error in load_NA_DNA (line 166)

Error in INITIATE (line 64)

Error in MAIN (line 66)

MATLAB:assertion:failed

Test_square.csv.txt

I cant load my .csv file here

Mac - Protocol.pdf missing

Hi! Awesome package :)

The file Protocol.pdf is missing in the Mac .zip file.
Maybe even add it to the top level, as an easy access online resource.

SNUPI on Linux?

I'm very excited by the rapid prototyping that SNUPI offers, however it seems like the program is Windows-only? I am not super familiar with Matlab, so perhaps I'm misunderstanding something, but is there a way to run the GUI on Linux or the code without the GUI within Matlab?

Mac - SNUPI2.1 - Mg Concentration

using the Mac OS version of snupi 2.1. on big sur 11.4.

changing the for magnesium concentration via:
ES_MG 20
does not appear to have any effect.

electrostatics is enabled: DO_ES 1

Mac - SNUPI2.1 - RMSF

using the Mac OS version of snupi 2.1. on big sur 11.4.
it seems like the rmsf values are not written to the occupancy field in the PDB file.
strain energy is correctly added to the b-factor field.

Mac - SNUPI2 - gen_PDB error

Hi, love to see how active the development is :)
I started testing Snupi2 right away. However, all runs with PDB or oxDNA file generation now fail. (tested 4 structures that worked with snupi1)

Here is the error message, I can send all files for testing if needed.

Unable to perform assignment because the size of the left side is 303750-by-1 and the size of the right side is 303090-by-1.
Error in PDB_Generator (line 317)
Error in gen_PDB (line 162)
Error in MAIN (line 343)
MATLAB:subsassigndimmismatch

SNUPI2.1 - Stacking

SNUPI prediction of blunt end stacking inside origami structures does not conform to our experimental observations.
Motives such as crossover stacks (illustration attached) open up instead of staying fairly compact (screenshots 1).
Staples broken at crossovers ("half crossover") also lead to distortion of the structures (screenshots 2).

High resolution cryo-EM data suggests that these regions remain stable and at most display a small lateral shift.
Would it be possible to include an "internal stacking basepair" step to the model to properly account for these motifs?
Or is there an alternative option to handle these situations? (have I maybe missed a setting?)
We can share design files and experimental data if required.

I have also noticed that these structures take significantly longer (2-3times) than structures of similar size.

"crossover stack":

1. open stack: 2. distorted feature:
   

using the Mac OS version of snupi 2.1. on big sur 11.4.

single-stranded loops

I encountered an issue trying to predict the structure of a design having single-stranded loops, using the Mac command line version with default parameters without providing a sequence file.

I ran tests using four variants of the 6-helix bundle provided in the EXAMPLES directory, which I modified to have: 1) a scaffold loop, 2) scaffold overhangs, 3) a staple loop, 4) staple overhangs:

The two variants having single-stranded staple overhangs or scaffold overhangs (multi-scaffold design required) work. For the two loop variants, I receive warnings of the following kind:

Please see complete logs and outputs in the attached zip file:
Outputs.zip

I would highly appreciate if you could fix this issue.

SNUPI on M1 chip

I have been trying to install SNUPI on my MacBook with a M1 chip. However, all of the Matlab compilers that are compatible with the current SNUPI builds are built for the intel chip. Do you have any recommendations?