# CODA-Map

**Repository Path**: hongxu66/CODA-Map

## Basic Information

- **Project Name**: CODA-Map
- **Description**: RNA homology modeling
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2022-11-10
- **Last Updated**: 2023-08-21

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# CodaMap User Manual

Thank you for choosing our program! This user manual will guide you through the steps to install, set up, and use our program. If you encounter any issues, please refer to this manual or contact our support team_


#### Requirement:
1. rmsd==1.4
2. biopython==1.78
3. numpy==1.20.3
4. x3-dna (1)
5. BRiQ (2)
  

#### Using the Program:

setup the path of x3-dna and BRiQ before running these scripts.

1.  cd example/
2.  python ../src/align.py 5Y87.pdb BA TEM.dbn TEM.mtx > out.ali
3.  python ../src/HOMORNA.py out.ali Template_Test.pdb0 TEM.dbn
4.  python ../src/BRiQ_task.py TEM.dbn
5.  run RNA-BRiQ to optimize the modeled RNA structure.

#### Troubleshooting:

If you encounter any issues with the program, refer to the error message displayed on the screen or check the program's help section for possible solutions.
If the issue persists, contact our support team for assistance.
Conclusion:
We hope this user manual has been helpful in getting you started with our program. If you have any questions or feedback, please do not hesitate to contact us.

#### References:

1. Lu, X.-J. & Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31, 5108–5121 (2003).

2. Xiong, P., Wu, R., Zhan, J. & Zhou, Y. Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement. Nat Commun 12, 2777 (2021).

3. Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science. 2017 Jan 20;355(6322):294-298.