4 research outputs found
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 Ã… 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.
Deeprank2
<h2>What's Changed</h2>
<ul>
<li>docs: Clarify Pytorch Geometric in README installation by @DarioMarzella in https://github.com/DeepRank/deeprank2/pull/508</li>
<li>Joss review 5983 jnwei by @jnwei in https://github.com/DeepRank/deeprank2/pull/523</li>
<li>fix: installation bug due to missing domain files by @gcroci2 in https://github.com/DeepRank/deeprank2/pull/525</li>
</ul>
<h2>New Contributors</h2>
<ul>
<li>@DarioMarzella made their first contribution in https://github.com/DeepRank/deeprank2/pull/508</li>
<li>@jnwei made their first contribution in https://github.com/DeepRank/deeprank2/pull/523</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/DeepRank/deeprank2/compare/v2.1.0...v2.1.1</p><p>The software paper "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning" has been submitted to <a href="https://joss.theoj.org/">JOSS</a>, and is currently <a href="https://github.com/openjournals/joss-reviews/issues/5983#issuecomment-1851075521">under review</a>. </p>