PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes

Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges

Deeprank2

What's Changed Fix fix: check only 1 pssm for variant queries by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/430 fix: pdb files with underscore in the filename gives unexpected query ids by @joyceljy in https://github.com/DeepRank/deeprank2/pull/447 fix: dataset_train inheritance warnings by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/461 fix: cast hse feature to float64 by @DanLep97 in https://github.com/DeepRank/deeprank2/pull/465 fix: readthedocs after deeprank2 renaming by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/472 fix: force scipy version for fixing deeprank2 installation by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/478 fix: warning messages for invalid data in test_dataset.py by @joyceljy in https://github.com/DeepRank/deeprank2/pull/442 fix: make scipy 1.11.2 work by @cbaakman in https://github.com/DeepRank/deeprank2/pull/482 Refactor refactor: inherit information from training set for valid/test sets by @joyceljy in https://github.com/DeepRank/deeprank2/pull/446 refactor: rename deeprankcore to deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/469 Build build: improve installation making use of pyproject.toml file only and setuptools by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/491 CI CI: decrease sensitivity of test_graph_augmented_write_as_grid_to_hdf5 by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/445 CI: fewer triggers by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/457 Docs docs: update README.md by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/443 docs: create tutorial README by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/455 docs: improve installation instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/452 docs: add tutorials for PPIs by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/434 docs: add tutorials for variants by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/459 docs: minor improvements to install instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/484 docs: type hinting and docstrings in molstruct by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/497 docs: joss paper by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/423 docs: clarify ppi scoring metrics and add doc strings and tests by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/498 docs: add performances table for deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/493 Style style: auto-scrape trailing whitespace upon save in VS code by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/483 Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.0.0...v2.1.

Deeprank2

What's Changed Fix fix: check only 1 pssm for variant queries by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/430 fix: pdb files with underscore in the filename gives unexpected query ids by @joyceljy in https://github.com/DeepRank/deeprank2/pull/447 fix: dataset_train inheritance warnings by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/461 fix: cast hse feature to float64 by @DanLep97 in https://github.com/DeepRank/deeprank2/pull/465 fix: readthedocs after deeprank2 renaming by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/472 fix: force scipy version for fixing deeprank2 installation by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/478 fix: warning messages for invalid data in test_dataset.py by @joyceljy in https://github.com/DeepRank/deeprank2/pull/442 fix: make scipy 1.11.2 work by @cbaakman in https://github.com/DeepRank/deeprank2/pull/482 Refactor refactor: inherit information from training set for valid/test sets by @joyceljy in https://github.com/DeepRank/deeprank2/pull/446 refactor: rename deeprankcore to deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/469 Build build: improve installation making use of pyproject.toml file only and setuptools by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/491 CI CI: decrease sensitivity of test_graph_augmented_write_as_grid_to_hdf5 by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/445 CI: fewer triggers by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/457 Docs docs: update README.md by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/443 docs: create tutorial README by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/455 docs: improve installation instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/452 docs: add tutorials for PPIs by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/434 docs: add tutorials for variants by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/459 docs: minor improvements to install instructions by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/484 docs: type hinting and docstrings in molstruct by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/497 docs: joss paper by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/423 docs: clarify ppi scoring metrics and add doc strings and tests by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/498 docs: add performances table for deeprank2 by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/493 Style style: auto-scrape trailing whitespace upon save in VS code by @DaniBodor in https://github.com/DeepRank/deeprank2/pull/483 Full Changelog: https://github.com/DeepRank/deeprank2/compare/v2.0.0...v2.1.