BindUP

BindUP predicts DNA and RNA binding proteins from protein three-dimensional structures by analyzing protein surface electrostatics and intrinsic surface properties.

Key Features:

• Non-homology-based approach: Uses electrostatic features and general protein surface properties rather than sequence homology to identify nucleic acid-binding capability.
• Electrostatic surface analysis: Evaluates electrostatic surface patches that are important for DNA and RNA interactions.
• Detection of proteins without known domains: Predicts nucleic acid-binding function in proteins lacking recognizable binding domains or similarity to established nucleic acid-binding proteins.
• Scalability and throughput: Supports single and batch processing to analyze multiple protein structures concurrently.
• Performance validation: Demonstrated high accuracy through testing on diverse datasets.

Scientific Applications:

• Identification of nucleic acid-binding proteins: Enables discovery of proteins with potential DNA- or RNA-binding functions from structural models or solved structures.
• Gene expression and regulation studies: Supports investigation of proteins involved in regulation of gene expression via nucleic acid interactions.
• Discovery of novel regulators: Facilitates finding previously unrecognized regulators that interact with DNA or RNA despite lacking canonical binding domains.

Methodology:

Computational prediction based on analysis of protein three-dimensional structures using electrostatic surface patch characterization and other intrinsic protein surface properties in a non-homology-based framework.