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Structure prediction

Molchanica has integrated structure prediction for proteins, small molecules, DNA, RNA, and ions, using OpenDDE. As a prerequisite to using this, install OpenDDE to a virtual environment accessibly by Molchanica using the included install_opendde script. Or install it on your own in a way where it is accessible on the system PATH environment variable. The linux setup script asks if it should install it.

structure prediction with OpenDDE

Note: OpenDDE is large due to its Torch model: Multiple GBs. If using the install script, it's installed to the following directory:

  • Windows: %LOCALAPPDATA%\molchanica\opendde-venv
  • macOS: ~/Library/Application Support/molchanica/opendde-venv
  • Linux: $XDG_DATA_HOME/molchanica/opendde-venv (else ~/.local/share/...)

To use it, click the Structure prediction button in the UI. In the window that opens, enter your amino acid sequence using single-letter identifiers, or your DNA sequence using "A", "C", "T", and "G" characters. (Neither are case-sensitive.) Click "Predict" to begin. The window will display cumulative run time, and update you on progress.

OpenDDE (And ML-based structure prediction in general) runs much faster with a GPU (I believe an Nvidia GPU only) is connected, and its drivers are installed and reasonably up to date. When installing OpenDDE manually, the method of installation determines whether it will work with GPU or not. If using the install script, it will detect if you have Nvidia drivers installed, and choose GPU if so; CPU if not.

Prediction may take minutes or hours depending on the size of the input sequence, your computer's capability, and other factors.