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Welcome to ProBufEx (Database for Protein Expression, Purification and Characterization)

This website allows you to search related buffers for protein purification and characterization using keywords or sentences, view related figures, and learn more about their features. In addition, you can search relevant recombinant protein expression conditions using keywords. Please note that this database was constructed using an LLM-based pipeline, and its estimated accuracy is shown below.

Functions:

• Buffer Function Search: Enter keywords, sentences or UniProt ID to find relevant results, including references, buffer details and functions, protein names, and DOIs. Each buffer entry is annotated with usage context and functional role, extracted and summarized by our AI-powered pipeline. Users can query the database using natural language input, which is interpreted through an embedding-based retrieval system to identify semantically relevant buffers.
• Buffer Components: Within our database, proteins were systematically annotated and grouped using 1,145 unique UniProtKB keywords, which are classified into seven categories: biological process, cellular components, coding sequence diversity, domain, ligand, molecular function, and post-translational modification. You can input a keyword to retrieve and display statistical data on buffer components.
• Protein Expression: Supports keyword-based queries using UniProtKB annotations and retrieves recombinant protein production data from published literature.

How to Use:

Navigate using the menu at the top. For searches, enter a term in the search box and submit.

Overview of this database statistics:

(A) Coverage of articles with successful data extraction, showing how many contain relevant buffer details or expression conditions.

(B) Accuracy of the extraction results evaluated on a test set of 40 randomly selected articles. Each instance was manually verified for correctness.

(C) Top 20 most frequent buffer categories identified in the database. Categories were assigned by a large language model (Mistral-Small-3.1-24B-Instruct).

(D) Distribution of expression systems used for recombinant protein production, showing both case counts and relative percentages.