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!