GARN3 User Manual

GARN3 is a Java application and it requires Java version 17 or higher.

GARN3 uses Fasta file for primary/secondary structures. Example:

>1E8O
gGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC
((((((((((((......)))))))....((((........)))))))))

Convert PDB file to GARN model

To create a file containing a GARN model from a PDB file: java -jar ./GARN3.jar PDBTOGARN ‹Name of molecule› ‹Fasta File› ‹Location of the PDB file›

Example:

java -jar ./GARN3.jar PDBTOGARN 1E8O 1E8O_fasta.txt 1E8O.pdb

Output two files : ‹Name of molecule›_GARN.csv with the position of nodes in 3D space, and ‹Name of molecule›_listNucleo.csv, to indicate the correspondance between nodes and nucleotides.

Predict molecules (run simulations)

To run the simulations and compute the sampling space: java -jar ./GARN3.jar GAME ‹Name of molecule› ‹Fasta File› ‹Number of solutions› [‹nbTour›] [EXP3|UCB] [‹GARN file of native structure›]

Notes:

• nbTour (optional): numeric override for the number of rounds per game. If omitted the program uses a default of 500 rounds (for large RNAs with >=100 players the default becomes 300). The value is parsed as a number (double) so integers like 500 or 750 are fine.
• Argument order: numberTest then optional nbTour, then optional algorithm (EXP3 or UCB), then optional reference GARN file for RMSD.

Simple example (no override):

java -jar ./GARN3.jar GAME 1E8O 1E8O_fasta.txt 10

Example overriding the number of rounds per game:

java -jar ./GARN3.jar GAME 1E8O 1E8O_fasta.txt 10 750

Example specifying algorithm and reference file (with nbTour omitted):

java -jar ./GARN3.jar GAME 1E8O 1E8O_fasta.txt 10 UCB 1E8O_GARN.csv

Example specifying both nbTour and algorithm and reference file:

java -jar ./GARN3.jar GAME 1E8O 1E8O_fasta.txt 10 750 EXP3 1E8O_GARN.csv

Output 10 files : GARN*‹Name of molecule›_0.csv, GARN*‹Name of molecule›1.csv, ..., GARN‹Name of molecule›_9.csv

If you wish to compute the sampling space and also compute RMSD, you need to provide a reference GARN model file as the final argument (see examples above). Use 0 in the algorithm position to let the program auto-select the algorithm, e.g.:

java -jar ./GARN3.jar GAME 1E8O 1E8O_fasta.txt 10 0 1E8O_GARN.csv

Output 11 files : GARN*‹Name of molecule›_0.csv, .. , & GARN*‹Name of molecule›_9.csv, ... and a ‹Name of molecule›_out.csv with the RMSD and the Maximum distance (to sort the sampling).

Calculate RMSD between predicted molecules

To compute the RMSD between GARN files (compare to one file): java -jar ./GARN3.jar RMSD ‹Name of molecule› ‹Reference GARN file› ‹GARN file 1› [GARN file 2 ...]

Example:

java -jar ./GARN3.jar RMSD 1E8O 1E8O_GARN.csv GARN_1E8O_1.csv GARN_1E8O_2.csv GARN_1E8O_3.csv GARN_1E8O_4.csv

Output 1 file: ‹Name of molecule›_rmsd.csv with the RMSD between the first file and others files.

Calculate TM-Score between predicted molecules

To compute the TM-Score between GARN files (compare to one file): java -jar ./GARN3.jar TMSCORE ‹Name of molecule› ‹GARN file of molecule 1› ‹GARN file of molecule 2› ...

Example:

java -jar ./GARN3.jar TMSCORE 1E8O 1E8O_GARN.csv GARN_1E8O_1.csv GARN_1E8O_2.csv GARN_1E8O_3.csv GARN_1E8O_4.csv

Output 1 file: ‹Name of molecule›_tmscore.csv with the RMSD between the first file and others files.

Calculate minimum and maximum distance

To compute the maximum distance in structure and sort the sampling: java -jar ./GARN3.jar SORT ‹Name of molecule› ‹GARN file of molecule 1› ‹GARN file of molecule 2› ...

Example:

java -jar ./GARN3.jar SORT 1E8O GARN_1E8O_1.csv GARN_1E8O_2.csv GARN_1E8O_3.csv GARN_1E8O_4.csv

Output 1 file: ‹‹Name of molecule››_sort.csv with the maximum distance for each solution.

Generate PDB/align/PyMOL outputs from GARN CSVs

To reproduce the GARNTOPDB flow:

java -jar ./GARN3.jar GARNTOPDB [‹Full PDB file› ‹listNucleo.csv file›] ‹game1.csv› [game2.csv ...]

Modes:

1. With PDB reference (using some full-atom experimental structure):

java -jar ./GARN3.jar GARNTOPDB 1E8O.pdb 1E8O_listNucleo.csv GARN_1E8O_0.csv GARN_1E8O_1.csv

2. Without PDB reference (first game file is used as reference):

java -jar ./GARN3.jar GARNTOPDB 1E8O_GARN.csv GARN_1E8O_0.csv GARN_1E8O_1.csv

Example:

java -jar ./GARN3.jar GARNTOPDB 1E8O.pdb 1E8O_listNucleo.csv 1E8O_GARN.csv GARN_1E8O_0.csv

Generated files:

1. GARN_*.pdb: PDB files generated from game CSVs.
2. <reference>.align: RMS alignment output for each generated structure against the selected reference.
3. If full reference mode is used: *_CG.pdb: reduced coarse-grained reference structure.
4. If full reference mode and PyMOL are available: *_CG.pse: optional PyMOL session file.

Contacts

When in doubt, you can contact jhonatansilva@usp.br or daniel.cordeiro@usp.br