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Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis

Python 66.24% Shell 3.16% Dockerfile 0.69% Jupyter Notebook 29.91%

protein protein-design

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timed-design's Issues

Calculate KL divergence between probabilities

Update streamlit cache

More information [in our docs](https://docs.streamlit.io/library/advanced-features/caching).
2024-01-31 13:24:56.783 `st.cache` is deprecated. Please use one of Streamlit's new caching commands,
`st.cache_data` or `st.cache_resource`. Based on this function's return value
of type `str`, we recommend using `st.cache_data`.

polar and charge fail with multichain input

DuplicateWidgetID: There are multiple identical st.selectbox widgets with key='option'.

To fix this, please make sure that the key argument is unique for each st.selectbox you create.

Traceback:
File "/scratch/channels/timed-design/ui.py", line 950, in <module>
    main(params)
File "/scratch/channels/timed-design/ui.py", line 904, in main
    slice_seq, slice_real, real_metrics = _draw_output_section(
File "/scratch/channels/timed-design/ui.py", line 481, in _draw_output_section
    option = st.selectbox(

Add sequence logo based on the probability distribution

Find all models in folder and predict with those

"rot" is appended to any predictions even with --predict_rotamers = False

Fix monte carlo not running all the time

Include polar and hydrophobic models

.fasta files not saved to specified output_dir

Output of predict.py saves all files but .fasta to directory specified in command line --path_to_output OUTPUT option:

python predict.py --path_to_dataset DATASET --path_to_model MODEL --path_to_output OUTPUT

.fasta files are saved to the current working directory

Zoom is broken

Takes the last value rather than the full number 72

[Feedback] Redesign Specific Residues only

I would love to be able to specify residues to design. Or full regions. If I have a structure, and I want to be able to (re)design a loop.

have different pages

https://blog.streamlit.io/introducing-multipage-apps/

Double check TIMED default model

Order UI Sections with functions

Disable run button after being pressed

Add documentation + sample code for UI

When PDB code of protein runs it is replaced with 1QYS

Charge and Polar have Ca and Cb channels inverted

Due to a bug in the training of the models, the training frames for the Charge and Polar models had the order:

[C, N, O, Cb, Ca, CHARGE/POLARITY]

Rather than

[C, N, O, Ca, Cb, CHARGE/POLARITY]

Which makes the Charge and Polar models unusable. A very hacky quick-fix of this would involve swapping the channels order at prediction time until we are able to spend time and computation retraining the models.

I propose to modify the function load_batch at

timed-design/design_utils/utils.py

Line 487 in abc6afa

def load_batch(

to include something like this ONLY FOR CHARGE AND POLAR MODELS:

# Extract frame from batch:
for i, (pdb_code, chain_id, residue_id, _) in enumerate(data_point_batch):
    # Extract frame:
    residue_frame = np.asarray(dataset[pdb_code][chain_id][residue_id][()])

    # Check if the frame has the correct shape (final dimension is 6) for swapping:
    if residue_frame.ndim == 4 and residue_frame.shape[-1] == 6:
        # Swap only the 4th and 5th channels (index 3 and 4)
        residue_frame[..., 3], residue_frame[..., 4] = residue_frame[..., 4].copy(), residue_frame[..., 3].copy()

    X[i] = residue_frame

    # Extract residue label:
    y[i] = dataset[pdb_code][chain_id][residue_id].attrs["encoded_residue"]

The charge and polar have a final dimension of 6

Integrate ESMFold and/or Omegafold

How to cite the project?

Hi @universvm, nice work!
I just want to ask if you have a preferred way to cite the project!
Thanks

Multichain is broken for TIMED models

May or may not be related to #36

Create Colab/Gradio Interface

Sequence logo makes everything sooooo slow

How much compute do you need to run a sequence logo? More than the compute available in the universe.

[Feedback] Add numbering to output sequence

A frequent residue numbering alongside the designed sequence. Perhaps every 10 or 5 residues have the residue number. It would make studying specific residue changes easier.

I was looking at specific residues which interact with a cofactor to see if TIMED offered alternative residues, but this involved counting along the sequence until we found the residues, a numbering would help:)

possible bug with rotamer categories

            flat_dataset_map, prediction_matrix, rotamers_categories=None

AssertionError: Prediction Matrix file TIMED1qys.csv does not exist