AlphaPulldown v2.0.1

AlphaPulldown 2.0.1 Release Notes

🚀 Automated Workflows with Snakemake

Introduced a streamlined pipeline for modeling tasks, leveraging Snakemake for automation, scalability, and reproducibility. Installation is now simplified with Docker/Singularity containers.

🔧 Unified Configuration Syntax

All AlphaPulldown modes now share a unified configuration syntax, simplifying input setup and enabling automatic sequence retrieval with UniProt IDs.

🛠️ Modular Backend Support

Reorganized the codebase to support multiple modeling backends flexibly. UniFold and AlphaLink2 are now integrated, with the potential to add more in the future.

🔗 Cross-Link-Driven Modeling

AlphaLink2 integration supports modeling with cross-linking mass spectrometry (XL-MS) data, enhancing the accuracy of complex structural models.

💾 Significant Storage Optimization

Achieved more than 90% reduction in storage through input feature and output file compression, promoting sustainability in large-scale modeling.

📦 ModelCIF Format Support

Models can now be stored in ModelCIF format, aligning with FAIR principles for improved model accessibility and simpler model deposition in databases.

🧩 Extended Modeling Capabilities

Increased flexibility with customizable modeling parameters, multimeric template support, and options to control MSA and template impact on predictions.

📊 Enhanced Analysis Pipeline

Enriched the analysis toolkit with additional evaluation metrics like average pLDDT and PAE scores at protein interfaces for better assessment of model confidence.

🔄 Improved Codebase and Documentation

Refactored code, introduced CI/CD pipelines, automated testing, and expanded documentation for a smoother user experience.

🌐 Repository of Precomputed Features

Released a web-based repository of precomputed input features for multiple model organisms, reducing redundant computations and accelerating workflows.

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🛠️ Corrections and Improvements from 2.0.0

• Added original run_alphafold.py to installed scripts
  You can now run the entire AlphaFold pipeline directly, ensuring compatibility and ease of use with existing workflows.

• Lifted Restriction on Output Directory Name Length
  The maximum length for output directory names is now extended to the maximum supported by your operating system, providing greater flexibility in naming conventions.

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As always, we appreciate your feedback and contributions to make AlphaPulldown even better.

Happy modeling!

AlphaPulldown v2.0.0

Release Notes

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🚀 Automated Workflows with Snakemake
Introduced a streamlined pipeline for modeling tasks, leveraging Snakemake for automation, scalability, and reproducibility. Installation is now simplified with Docker/Singularity containers.

🔧 Unified Configuration Syntax
All AlphaPulldown modes now share a unified configuration syntax, simplifying input setup and enabling automatic sequence retrieval with UniProt IDs.

🛠️ Modular Backend Support
Reorganized codebase to support multiple modeling backends flexibly. UniFold and AlphaLink2 are now integrated, with the potential to add more in the future.

🔗 Cross-Link-Driven Modeling
AlphaLink2 integration supports modeling with cross-linking mass spectrometry (XL-MS) data, enhancing the accuracy of complex structural models.

💾 Significant Storage Optimization
Achieved more than 90% reduction in storage through input feature and output file compression, promoting sustainability in large-scale modeling.

📦 ModelCIF Format Support
Models can now be stored in ModelCIF format, aligning with FAIR principles for improved model accessibility and simpler model deposition in databases.

🧩 Extended Modeling Capabilities
Increased flexibility with customizable modeling parameters, multimeric template support, and options to control MSA and template impact on predictions.

📊 Enhanced Analysis Pipeline
Enriched the analysis toolkit with additional evaluation metrics like average pLDDT and PAE scores at protein interfaces for better assessment of model confidence..

🔄 Improved Codebase and Documentation
Refactored code, introduced CI/CD pipelines, automated testing, and expanded documentation.

🌐 Repository of Precomputed Features
Released a web-based repository of precomputed input features for multiple model organisms, reducing redundant computations and accelerating workflows.

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AlphaPulldown v2.0.0b6

1. Update biopython to the latest version
2. Instructions on how to install cpp4 within the analysis container
3. Fix run_multimer_jobs.py relative paths
4. Remove run_alphafold.py and stereo_chemicsl_props.py from installation
5. Made compatible with python>3.10
6. Multiple minor code optimizations

AlphaPulldown v2.0.0b5

There is only a single fix: generating features with mmseqs2 previously did not work because of #399
Many thanks to kashyapchhatbar for finding this out and reporting!

AlphaPulldown v2.0.0b4

1. Merged updated manual, credits to @gilep
2. Fixed bug: predictions for homo-oligomers using whole ranges.
3. ranking_debug.json: save iptm for multimers OR ptm for monomers.
4. Added modelcif dependency to the pulldown.docker file and github actions.
5. Used system.entities instead of system.target_entities for convert_to_modelcif.py.
6. Added tests for modelcif and run_multimer_jobs.py.
7. Used the correct docker image from kosinskilab for the analysis pipeline.

AlphaPulldown 2.0.0 beta v3

1. Removed dependencies from the result pickles.
2. Fixed the "key error" while running the create_notebook.py. Thanks for the help from @DimaMolod and the report from @gebauer
3. Beautified and updated the manual. Thanks for the work from @gilep . The updated manual is close to be finished and will be merged soon after the release once it's proof-read.
4. Updated the singularity image of the analysis pipeline so that it handles the exceptions caused by monomeric models.

You could download this version by running pip install alphapulldown==2.0.0b3

Note: please download the new singularity image: alpha-analysis.sif . Since all the dependencies in the result files are removed in this version, there is no need to build two singularity images for jax version 0.3 and jax version 0.4, as in the previous versions.

If you have created models using the versions prior to the alphapulldown==2.0.0b3, please rerun the run_multimer_jobs.py before using the updated the singularity image. The rerun will be quick as only the result pickles are to be changed.

AlphaPulldown 2.0.0 beta v2

New features added:

1. Added calculation of average PAE value of interface residues to analysis_pipeline
2. Added calculation of average plDDT value of interface residues to analysis_pipeline
3. Added calculation of binding energy via pyRosetta value of interfaces to analysis_pipeline
4. Updated pyTest thanks for the help from @DimaMolod

Bugs fixed:

1. Fixed crashes caused by monomer #312
2. Fixed wrong contents in the plotted PAE images #312
3. Fixed wrong calculation of iptm-ptm and iptm scores when using padding mode #312

Notice:
Apart from installing the beta version of alphapulldown from pypi, using pip install alphapulldown==2.0.0b2, please re-download the alpha-analysis singularity images again this time.
If your results are from AlphaPulldown prior to version 1.0.0, please use the link: alpha-analysis_jax_0.3.sif.
If your results are from AlphaPulldown with version >=1.0.0, please use the link: alpha-analysis_jax_0.4.sif.

AlphaPulldown 2.0.0 beta v1

New features added:

1. Refactorised the codes; introduced folding_backend #303 thanks for the help from @maurerv and @DimaMolod
2. Allow the user to pad input matrices to desired number of MSAs and desired number of residues to speed up overall modelling process and avoid unnecessary re-compiling of AlphaFold neural network.
3. New way of modelling with customised structure templates without the need of recalculating the features again. #268
4. Separated post-modelling processes from prediction process #297 by @DimaMolod
5. Supports full mmseqs2 mode i.e. without the need of local structural template database when using mmseqs mode #233

Bugs fixed:

1. Fixed incorrect colour scheme when ploting structures in jupyter-notebook #304 thanks for the help from @gchojnowski and report from @gilep
2. Fixed operands broadcast error when the features are created by mmseqs2 #287 thanks for the report from @Qrouger
3. Updated alpha-analysis.sif to avoid crashes when no model satisfies the cutoff value #307
4. Fix the config.cfg to avoid installing tensorflow versions that are not compatible with GPUs without latest CUDA. #298 Thanks for the help from @kashyapchhatbar

Notice:
Apart from installing the beta version of alphapulldown from pypi, using pip install alphapulldown==2.0.0b1, please re-download the alpha-analysis singularity images again.
If your results are from AlphaPulldown prior to version 1.0.0, please use the link: alpha-analysis_jax_0.3.sif.
If your results are from AlphaPulldown with version >=1.0.0, please use the link: alpha-analysis_jax_0.4.sif.

AlphaPulldown v1.0.4

Bugs fixed:

1. Fixed the incorrectly installed alphafold submodule #232 many thanks for the help from @aokosinska
2. Fixed the import issue from biopython #234 and #231 Thanks for the help from @aokosinska and @grandrea
3. Fixed the create_notebook.py issue #211

AlphaPulldown v1.0.3

Bugs fixed:

1. Fixed the incorrectly installed AlphaLink2 submodule #224
2. removed jax dependency when saving results pickles. credits to @DimaMolod 06461b8