├── .gitignore ├── DDGScan ├── GUI ├── EasyFoldx │ └── 1PAG.pdb ├── GUI.py ├── README.md ├── multiple_threads_foldx_positionscan.py ├── pdb2seq.py ├── prepare4buildmodel.py └── prepare4scan.py ├── LICENSE ├── README.md ├── ddgscan ├── __init__.py └── utils │ ├── __init__.py │ ├── aa_index.py │ ├── abacus.py │ ├── abacus2_lr.py │ ├── abacus2_nn.py │ ├── autofix.py │ ├── common.py │ ├── data │ ├── lr │ │ └── abacus2_ddg_param.csv │ └── nn │ │ ├── abacus2_nn_0.pt │ │ ├── abacus2_nn_1.pt │ │ ├── abacus2_nn_2.pt │ │ ├── abacus2_nn_3.pt │ │ ├── abacus2_nn_4.pt │ │ ├── abacus2_nn_5.pt │ │ ├── abacus2_nn_6.pt │ │ ├── abacus2_nn_7.pt │ │ ├── abacus2_nn_8.pt │ │ └── abacus2_nn_9.pt │ ├── foldx.py │ ├── grape_phaseI.py │ ├── io.py │ ├── judge.py │ ├── list_distribute.py │ ├── mdrelax.py │ ├── modeller_loop.py │ ├── multimer_scan.py │ ├── post_analysis_and_plot.py │ └── rosetta.py ├── environment.yml ├── grape-fast.py ├── img ├── results_toc.png └── workflow.png ├── multimer_scan.py ├── parallel_sites.py ├── requirements.txt ├── scripts ├── cart2.script └── inspectmutation.py ├── setup.py └── utils ├── __init__.py ├── aa_index.py ├── abacus.py ├── abacus2_lr.py ├── abacus2_nn.py ├── autofix.py ├── common.py ├── data ├── lr │ └── abacus2_ddg_param.csv └── nn │ ├── abacus2_nn_0.pt │ ├── abacus2_nn_1.pt │ ├── abacus2_nn_2.pt │ ├── abacus2_nn_3.pt │ ├── abacus2_nn_4.pt │ ├── abacus2_nn_5.pt │ ├── abacus2_nn_6.pt │ ├── abacus2_nn_7.pt │ ├── abacus2_nn_8.pt │ └── abacus2_nn_9.pt ├── foldx.py ├── grape_phaseI.py ├── io.py ├── judge.py ├── list_distribute.py ├── mdrelax.py ├── modeller_loop.py ├── multimer_scan.py ├── post_analysis_and_plot.py └── rosetta.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/.gitignore -------------------------------------------------------------------------------- /DDGScan: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/DDGScan -------------------------------------------------------------------------------- /GUI/EasyFoldx/1PAG.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/EasyFoldx/1PAG.pdb -------------------------------------------------------------------------------- /GUI/GUI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/GUI.py -------------------------------------------------------------------------------- /GUI/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/README.md -------------------------------------------------------------------------------- /GUI/multiple_threads_foldx_positionscan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/multiple_threads_foldx_positionscan.py -------------------------------------------------------------------------------- /GUI/pdb2seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/pdb2seq.py -------------------------------------------------------------------------------- /GUI/prepare4buildmodel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/prepare4buildmodel.py -------------------------------------------------------------------------------- /GUI/prepare4scan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/GUI/prepare4scan.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/README.md -------------------------------------------------------------------------------- /ddgscan/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /ddgscan/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /ddgscan/utils/aa_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/aa_index.py -------------------------------------------------------------------------------- /ddgscan/utils/abacus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/abacus.py -------------------------------------------------------------------------------- /ddgscan/utils/abacus2_lr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/abacus2_lr.py -------------------------------------------------------------------------------- /ddgscan/utils/abacus2_nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/abacus2_nn.py -------------------------------------------------------------------------------- /ddgscan/utils/autofix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/autofix.py -------------------------------------------------------------------------------- /ddgscan/utils/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/common.py -------------------------------------------------------------------------------- /ddgscan/utils/data/lr/abacus2_ddg_param.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/lr/abacus2_ddg_param.csv -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_0.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_0.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_1.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_1.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_2.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_2.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_3.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_3.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_4.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_4.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_5.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_5.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_6.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_6.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_7.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_7.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_8.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_8.pt -------------------------------------------------------------------------------- /ddgscan/utils/data/nn/abacus2_nn_9.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/data/nn/abacus2_nn_9.pt -------------------------------------------------------------------------------- /ddgscan/utils/foldx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/foldx.py -------------------------------------------------------------------------------- /ddgscan/utils/grape_phaseI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/grape_phaseI.py -------------------------------------------------------------------------------- /ddgscan/utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/io.py -------------------------------------------------------------------------------- /ddgscan/utils/judge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/judge.py -------------------------------------------------------------------------------- /ddgscan/utils/list_distribute.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/list_distribute.py -------------------------------------------------------------------------------- /ddgscan/utils/mdrelax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/mdrelax.py -------------------------------------------------------------------------------- /ddgscan/utils/modeller_loop.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/modeller_loop.py -------------------------------------------------------------------------------- /ddgscan/utils/multimer_scan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/multimer_scan.py -------------------------------------------------------------------------------- /ddgscan/utils/post_analysis_and_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/post_analysis_and_plot.py -------------------------------------------------------------------------------- /ddgscan/utils/rosetta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/ddgscan/utils/rosetta.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/environment.yml -------------------------------------------------------------------------------- /grape-fast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/grape-fast.py -------------------------------------------------------------------------------- /img/results_toc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/img/results_toc.png -------------------------------------------------------------------------------- /img/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/img/workflow.png -------------------------------------------------------------------------------- /multimer_scan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/multimer_scan.py -------------------------------------------------------------------------------- /parallel_sites.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/parallel_sites.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/cart2.script: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/scripts/cart2.script -------------------------------------------------------------------------------- /scripts/inspectmutation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/scripts/inspectmutation.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/setup.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /utils/aa_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/aa_index.py -------------------------------------------------------------------------------- /utils/abacus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/abacus.py -------------------------------------------------------------------------------- /utils/abacus2_lr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/abacus2_lr.py -------------------------------------------------------------------------------- /utils/abacus2_nn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/abacus2_nn.py -------------------------------------------------------------------------------- /utils/autofix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/autofix.py -------------------------------------------------------------------------------- /utils/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/common.py -------------------------------------------------------------------------------- /utils/data/lr/abacus2_ddg_param.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/lr/abacus2_ddg_param.csv -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_0.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_0.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_1.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_1.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_2.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_2.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_3.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_3.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_4.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_4.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_5.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_5.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_6.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_6.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_7.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_7.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_8.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_8.pt -------------------------------------------------------------------------------- /utils/data/nn/abacus2_nn_9.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/data/nn/abacus2_nn_9.pt -------------------------------------------------------------------------------- /utils/foldx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/foldx.py -------------------------------------------------------------------------------- /utils/grape_phaseI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/grape_phaseI.py -------------------------------------------------------------------------------- /utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/io.py -------------------------------------------------------------------------------- /utils/judge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/judge.py -------------------------------------------------------------------------------- /utils/list_distribute.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/list_distribute.py -------------------------------------------------------------------------------- /utils/mdrelax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/mdrelax.py -------------------------------------------------------------------------------- /utils/modeller_loop.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/modeller_loop.py -------------------------------------------------------------------------------- /utils/multimer_scan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/multimer_scan.py -------------------------------------------------------------------------------- /utils/post_analysis_and_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/post_analysis_and_plot.py -------------------------------------------------------------------------------- /utils/rosetta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JinyuanSun/DDGScan/HEAD/utils/rosetta.py --------------------------------------------------------------------------------