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.
🛠️ Corrections and Improvements from 2.0.0
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Added original
run_alphafold.pyto 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.
As always, we appreciate your feedback and contributions to make AlphaPulldown even better.
Happy modeling!