PINDER: The Protein INteraction Dataset and Evaluation Resource#
Contents:
- Getting started
- Examples
- Pinder index
- Pinder system
- PinderSystem API - base class representing
Structure’s in a pinder entry - Classify system difficulty based on degree of conformational shift in unbound and bound
- Illustrating utilities available in
Structureinstances - Can also filter “in place” rather than returning a copy (a la pandas)
- Create masked unbound complex aligned to bound for apo
- Structures have
resolved_pdb2uniprotandresolved_uniprot2pdbproperties - Case with multiple available apo structures
- Classify system difficulty based on degree of conformational shift in unbound and bound
- A bunch of other features of the
Structureclass are illustrated below
- PinderSystem API - base class representing
- Pinder loader
- Pinder eval
- FAQ: cropped monomer superposition
- Examine monomer shapes prior to cropping or superposition
- Single alternative monomer use-case without cropping
- With cropping such that apo and holo have the same shapes
- Why are these atoms missing in the apo, but present in the holo structure?
- What if we need them to be identical shapes?
- We specified
monomer_typesapo, but got a tuple of structures that included the predicted complex, why?
- MLSB PINDER Challenge
- API reference
- Subpackages
- pinder.core package
- pinder.data package
- Subpackages
- Submodules
- pinder.data.alignment_utils module
- pinder.data.apo_utils module
- pinder.data.config module
- pinder.data.csv_utils module
- pinder.data.find_transitive_hits module
- pinder.data.foldseek_utils module
- pinder.data.get_alignment_similarity module
- pinder.data.get_annotations module
- pinder.data.get_apo module
- pinder.data.get_clusters module
- pinder.data.get_data module
- pinder.data.get_dimers module
- pinder.data.get_splits module
- pinder.data.get_test_set module
- pinder.data.graph_utils module
- pinder.data.rcsb_rsync module
- pinder.data.run module
- pinder.data.system module
- Module contents
- pinder.eval package
- pinder.methods package
- Subpackages
- Pinder abstractions
- FAQ
- Is there a sequence database available?
- Can
pinderbe used to detect steric clashes? - What do holo, apo, native, and predicted structures within
PinderSystemmean? - For some protein pairs, when I extract the apo and holo structures and align their sequence, the results don’t have the same atoms and/or sequence. How can I align monomers such that all have the same shape?
- How can I use the evaluation harness outside of a
pindercontext? - Do I have to use the
pinderloader? How can I write my own loader?
- Limitations
- Changelog