AlphaPulldown v2.0.0
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 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.