AlphaPulldown v2.1.5

1. Reduced sized of alphafold2 and alphalink docker containers
2. Added flag validator that prevents using eg alphafold2 flags with alphafold3 backend
3. Drop redundant flags from run_multimer_jobs.py so the scirpt works with the new validator (credits to @Qrouger)
4. Use ccd instead of cached_ccd in af3 backend (again, thanks to @Qrouger !)
5. Use dense MSA representation when using alphafold2 features with alphafold3 backend
6. Move inputs parser to a separate repository
7. Renamed alphafold backend into alphafold2 (including name of the --fold-backend flag)

AlphaPulldown v2.1.4

1. Add options to save embeddings and distogram from AF3 backend.
2. Add backend-specific flag validator to run_structure_prediction.py (now you can't run backends with wrong flags!).
3. Sync alphafold2 module to the latest version (choose number of cores for MSA tools, global refactoring with pyink, etc).
4. Trim and simplify docker instructions for AlphaLink2.
5. Renamed 'fold' container into 'alphafold2'.
6. Renamed 'pulldown' dockerfile into 'alphafold2'.
7. Updated documentation.

AlphaPulldown v2.1.1

Fixed issues #524 and #528

AlphaPulldown v2.1.0

Release notes

• AlphaFold3 data pipeline support: You can now generate AlphaFold3-compatible data.json feature files directly from FASTA files for proteins, DNAs and RNAs using the create_individual_features.py script with the --data_pipeline flag.

• Support for all AlphaFold3 feature types: The pipeline now accepts all types of AlphaFold3 data.json feature files—including proteins, DNA, RNA, (also, with PTMs) and ligands. Place these files in the features directory and ensure they have a .json extension in --protein_lists when using run_multimer_jobs.py or in --input for run_structure_prediction.py.

• AlphaFold2 and AlphaFold3 compatibility: You can now mix AlphaFold2 .pkl features (including "chopped" proteins defined with residue ranges) and AlphaFold3 .json features in the same prediction run.

AlphaPulldown v2.0.4

1. Update modelcif converter to use the latest modelcif version (issue #508 fixed in 4baca88)
2. Updated documentation to use specific jax version (issue #504) and latest URL for uniref30 (issue #338)
3. Randomly generate random_seed depending on the backend in use (issue #489)
4. Do not adjust filtering criteria if multimeric templates are not used (b6fb69d)
5. New tests for creating monomeric and multimeric features dictionaries

AlphaPulldown v2.0.3

• Bug Fix: Fixed a bug affecting the pairing of sequences from the same species, which prevented pairing altogether. This issue was present in AlphaPulldown versions released since August 2023 and may have reduced prediction accuracy.
• Database Note: The MSA features in our database currently lack the pairing information needed to pair sequences from the same species. Using these features may also impact accuracy, please generate features yourself using the latest AlphaPulldown version. We are actively working on a fix.

AlphaPulldown v2.0.2

🚀 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.

🛠️ Corrections and Improvements from 2.0.0

Restored run_alphafold.py Script
The original run_alphafold.py script is now included in the installation, allowing seamless execution of the full AlphaFold pipeline while ensuring compatibility with existing workflows.

Expanded Output Directory Name Support
The maximum length for output directory names is now extended to the limits imposed by your operating system, providing greater flexibility in naming conventions.

Experimental AlphaFold3 Backend Support
Added initial support for the AlphaFold3 backend, expanding future modeling possibilities.

Unified Snakemake Compatibility for All Backends
All modeling backends, including UniFold and AlphaLink2, can now be used seamlessly within the Snakemake pipeline.

Bug Fix: Remote MMseqs Execution
Fixed an issue where the pipeline attempted to run remote MMseqs even when local MSA files were provided.

As always, we welcome your feedback and contributions to improve AlphaPulldown!

🚀 Happy modeling!

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.

---

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