Rider_Dependent_Databases_v1.0_beta

This repository contains the essential alignment database and dependency submodules required for the operation of Rider, a computational tool designed for RNA viral protein identification and analysis. This collection serves as a comprehensive resource for validating structural similarities between Rider-predicted candidates and known reference RNA viral proteins, specifically focusing on RNA-dependent RNA polymerase (RdRP). Related Publication:The preprint describing the Rider methodology and this dataset is available on bioRxiv: Title: Expanding the RNA Virus Universe by Scalable Structure-Guided Discovery (2025-11-29) Link: https://doi.org/10.1101/2025.11.24.690314 Key Components: 1. Rider Structure Database: Contains 217,762 RdRP protein structures in .pdb format.Note: This version includes a broad collection of structures without strict filtering for core domains. A refined sub-database dedicated exclusively to the RdRP core domain will be introduced in future updates. 2. Integrated Submodules: ESM2 (35M parameters): Pre-trained weights utilized for protein sequence tokenization and embedding generation.ESMFold (v1 model): Model weights for high-accuracy protein structure prediction.Foldseek: Binary/Executable components for fast and sensitive structural alignment. Usage Note:This version is released primarily to support the peer review process of the Rider manuscript. The repository will be updated with refined datasets and documentation upon the official publication of Rider.