GDS-fold

GDS-fold is a protein simulation toolkit centered on contact-map-driven exploration of dynamics using Graph Driven Search (GDS). At its core, it uses contact map representations to build sequences of states that represent folding pathways. Extension of this can include studying specific large conformational changes and perhaps even protein-protein dynamics.

Typical Workflow

1. Define a protein system and define its initial and final contact-map states.
2. Run GDS to find pathways between these states in contact-map space.
3. Use the contact-map states to reconstruct a sequence of alpha-trace coordinates (or even all-atom strutures).
4. Use the intermediate states to evaluate and describe the dynamical process.

Install

python -m pip install -U pip
python -m pip install .

For development (editable install):

python -m pip install -e . --no-build-isolation

To build a wheel locally:

python -m pip install -U build
python -m build

Docs

Install docs dependencies:

python -m pip install .[docs]

Build HTML docs directly with Sphinx:

python -m sphinx -b html docs/source docs/_build/html

Built docs are written to:

docs/_build/html