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Merge pull request #8 from torchmd/mutant_info
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added mutant info
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@MaciejMajew
MaciejMajew authored Jul 13, 2023
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Expand Up @@ -34,6 +34,7 @@ Here are all the native structures obtained experimentally that we used as refer
## Training data

Here you can find all the training data used for all protein systems, containing alpha-carbon coordinates, forces, deltaforces and embeddings. All arrays are stored in `.npy` arrays.
`.xtc` files with starting positions you can find in this repo in `Tutorials/starting_xtc/`

| Protein | Coordinates| Forces | Deltaforces | Embeddings |
| --------- | :----: | :----------: | :---------: | :------: |
Expand Down Expand Up @@ -68,3 +69,20 @@ Here you can find all the coarse-grained trajectories produced for all protein s
| Protein G | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/proteing_cgtraj_protspecific.tar.gz) | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/proteing_cgtraj_multiprotein.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/proteing_ca.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/proteing_ca_top_dih.psf) |
| a3D | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/a3d_cgtraj_protspecific.tar.gz) | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/a3d_cgtraj_multiprotein.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/a3d_ca.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/a3d_ca_top_dih.psf) |
| Lambda-repressor | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/lambda_cgtraj_protspecific.tar.gz) | [Link](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/lambda_cgtraj_multiprotein.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/lambda_ca.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data/cg_trajectories/lambda_ca_top_dih.psf) |

## Mutant trajectories

Here you can find all the coarse-grained trajectories produced for experiment with the mutants of invesigated proteins. All trajectories are stored in `.xtc` format. The trajectories contain coordinates for all CA atoms of each protein. PDB and PSF files are also provided as topology files to load trajectories. In order to match the lenght of the reference protein mutants `1P7J` and `2N35` were extended by 1-2 residues. For these cases `PDB` file contains a modified version of the protein and `PDB_org` contains CA representation of the experimental structure asociated with this code.
| Protein | Mutant PDBid | Trajectories | PDB | PSF | PDB_org |
| --------- | :-----------: | :----------: | :---------: | :------: | :------: |
| BBL | 1BAL | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/bbl_1BAL_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/bbl_1BAL.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/bbl_1BAL.psf) | |
| Protein B | 1GAB | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_1GAB_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_1GAB.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_1GAB.psf) | |
| Protein B | 2N35 | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_2N35_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_2N35.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_2N35.psf) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/proteinb_2N35_org.pdb) |
| Homeodomain | 1DU0 | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1DU0_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1DU0.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1DU0.psf) | |
| Homeodomain | 1P7I | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7I_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7I.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7I.psf) | |
| Homeodomain | 1P7J | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7J_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7J.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7J.psf) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_1P7J_org.pdb) |
| Homeodomain | 2HOS | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_2HOS_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_2HOS.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_2HOS.psf) | |
| Homeodomain | 6M3D | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_6M3D_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_6M3D.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/homeodomain_6M3D.psf) | |
| a3D | 2MTQ | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/a3d_2MTQ_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/a3d_2MTQ.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/a3d_2MTQ.psf) | |
| Lambda-repressor | 1LLI | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_1LLI_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_1LLI.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_1LLI.psf) | |
| Lambda-repressor | 3KZ3 | [Link](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_3KZ3_traj.tar.gz) | [PDB](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_3KZ3.pdb) | [PSF](http://pub.htmd.org/protein_thermodynamics_data_mutants/mutants/lambda_3KZ3.psf) | |

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