https://github.com/bioinfomachinelearning/gd-multimer
Stochastic gradient descent method for reconstructing protein multimer structures from inter-chain contacts/distances
https://github.com/bioinfomachinelearning/gd-multimer
Last synced: 2 months ago
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Stochastic gradient descent method for reconstructing protein multimer structures from inter-chain contacts/distances
- Host: GitHub
- URL: https://github.com/bioinfomachinelearning/gd-multimer
- Owner: BioinfoMachineLearning
- License: apache-2.0
- Created: 2022-06-10T02:38:50.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-08-08T03:57:07.000Z (over 3 years ago)
- Last Synced: 2025-09-09T16:34:18.093Z (8 months ago)
- Language: Python
- Size: 1.19 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GD-multimer
Stochastic gradient descent method for reconstructing protein multimer structures from inter-chain contacts/distances
** Download GD-Multimer package (short path is recommended)**
```
git clone git@github.com:BioinfoMachineLearning/GD-multimer.git
(If fail, try username) git clone https://github.com/BioinfoMachineLearning/GD-multimer.git
cd GFOLD
```
** How to run the code:**
```
For dimers using contact:
python ./scripts/docking_new.py target_name first_chain second_chain res_file output_dir weight_file top_num
example:
python ./scripts/docking_new.py T0965A_T0965B GD_tools/pdb_homo/chains/T0965A.pdb GD_tools/pdb_homo/chains/T0965B.pdb ../output_distance/T0965A_T0965B_con.rr ./ ./talaris2013.wts all
```
```
For dimers using distance:
python ./scripts/docking_new_dist.py target_name first_chain second_chain res_file output_dir weight_file thre
example:
python ./scripts/docking_new_dist.py T0965A_T0965B GD_tools/pdb_homo/chains/T0965A.pdb GD_tools/pdb_homo/chains/T0965B.pdb ../output_distance/T0965A_T0965B_dist.rr ./ ./talaris2013.wts 6
```
```
For multimers using contact:
python ./scripts/docking_gd_parallel_multi.py target_name num_of_chains first_chain second_chain third_chain ... nth_chain res_file output_dir weight_file top_num
example:
python ./scripts/docking_gd_parallel_multi.py T1034 4 /home/esdft/Downloads/pdbs/initial_start_multi/T1034A.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034B.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034C.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034D.pdb /home/esdft/Downloads/output_distance/T1034o.rr /home/esdft/Downloads/pdbs/ ./talaris2013.wts all
```
```
For multimers using distance:
python ./scripts/docking_gd_parallel_multi_dist.py target_name num_of_chains first_chain second_chain third_chain ... nth_chain res_file output_dir weight_file thre
example:
python ./scripts/docking_gd_parallel_multi_dist.py T1034 4 /home/esdft/Downloads/pdbs/initial_start_multi/T1034A.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034B.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034C.pdb /home/esdft/Downloads/pdbs/initial_start_multi/T1034D.pdb /home/esdft/Downloads/output_distance/T1034o.rr /home/esdft/Downloads/pdbs/ ./talaris2013.wts 36
```