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| sequences: | |
| - protein: | |
| id: [A, B] | |
| sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ | |
| msa: ./seq1.a3m | |
| - ligand: | |
| id: [C, D] | |
| ccd: SAH | |
| - ligand: | |
| id: [E, F] |
ljmartin
/ combiningKd_simulation.ipynb
Created
November 20, 2024 06:42
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ljmartin
/ modal-chai1.py
Created
November 27, 2024 22:23
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| import modal | |
| image = ( | |
| modal.Image.debian_slim() | |
| .pip_install("uv") | |
| .run_commands("uv pip install --system --compile-bytecode chai_lab==0.4.2") | |
| .run_commands('mkdir -p /usr/local/lib/python3.11/site-packages/downloads/models_v2') | |
| .apt_install("wget") | |
| .run_commands('wget -O /usr/local/lib/python3.11/site-packages/downloads/conformers_v1.apkl https://chaiassets.com/chai1-inference-depencencies/conformers_v1.apkl') | |
| .run_commands('wget -O /usr/local/lib/python3.11/site-packages/downloads/models_v2/trunk.pt https://chaiassets.com/chai1-inference-depencencies/models_v2/trunk.pt') |
ljmartin
/ golicnik schnell stroberg example.ipynb
Created
January 20, 2025 04:59
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ljmartin
/ minrepro_conformer_dependence.ipynb
Created
March 14, 2025 05:38
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ljmartin
/ modal_bioemu.py
Created
March 25, 2025 09:10
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| import modal | |
| image = ( | |
| modal.Image.micromamba(python_version="3.10") | |
| .apt_install('gcc') | |
| .apt_install('git', 'wget') | |
| .micromamba_install('openmm==8.0.0', 'pdbfixer','kalign2=2.04', 'hhsuite=3.3.0', | |
| 'mmseqs2', channels=['conda-forge', 'bioconda']) | |
| .run_commands('pip install "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"') | |
| .run_commands('pip install "colabfold[alphafold]"') |
ljmartin
/ expect_max_guess.py
Created
May 2, 2025 04:13
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| import pandas as pd | |
| from rdkit import Chem | |
| from rdkit.Chem import AllChem | |
| from rdkit.Chem import rdMolDescriptors | |
| from rdkit.Chem import AllChem, rdMolDescriptors, rdMolAlign, rdMolTransforms | |
| import numpy as np | |
| from tqdm.notebook import tqdm |
ljmartin
/ HCTBlog.ipynb
Last active
June 18, 2025 23:39
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ljmartin
/ GBN2Blog.ipynb
Created
August 23, 2025 23:14
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ljmartin
/ 4Y73-XPY.protein.cif
Created
March 26, 2026 00:04
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| data_structure | |
| # | |
| loop_ | |
| _atom_site.group_PDB | |
| _atom_site.type_symbol | |
| _atom_site.label_atom_id | |
| _atom_site.label_alt_id | |
| _atom_site.label_comp_id | |
| _atom_site.label_asym_id | |
| _atom_site.label_entity_id |