How to Use PRODIGY (PROtein binDIng enerGY) Online
Try PROtein binDIng enerGY (PRODIGY)
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PRODIGY: A Tool for Predicting Protein Binding
PRODIGY (PROtein binDIng enerGY prediction) is a powerful computational tool for predicting the binding affinity of protein-protein complexes from their 3D structures. It is used to understand molecular interactions, guide therapeutic development, and engineer protein complexes.
The tool estimates the binding free energy (ΔG) and dissociation constant (Kd) based on structural properties, making it simple, robust, and fast. In comparisons with other state-of-the-art predictors, PRODIGY has demonstrated a top performance.
How PRODIGY Works
PRODIGY's predictive model is based on a contact-based approach that relies on the number and type of intermolecular residue-residue contacts at the interface, in combination with properties of the non-interacting surface.
Input: The tool accepts 3D protein-protein complex structures in PDB or mmCIF format.
Contact Analysis: PRODIGY calculates the binding free energy and dissociation constant by analyzing the intermolecular contacts within a user-defined distance threshold.
Detailed Report: It provides a detailed report that includes the number and type of contacts, the percentage of charged and polar residues, and residue-specific interactions.
This method is highly efficient and can be used to predict chemical shifts for a large number of structures, such as those generated from molecular dynamics trajectories.
What is Tamarind Bio?
Tamarind Bio is a pioneering no-code bioinformatics platform built to democratize access to powerful computational tools for life scientists and researchers. Recognizing that many cutting-edge machine learning models are often difficult to deploy and use, Tamarind provides an intuitive, web-based environment that completely abstracts away the complexities of high-performance computing, software dependencies, and command-line interfaces.
The platform is designed provide easy access to biologists, chemists, and other researchers who may not have a background in programming or cloud infrastructure but want to run experimental models with their data. Key features include a user-friendly graphical interface for setting up and launching experiments, a robust API for integration into existing research pipelines, and an automated system for managing and scaling computational resources. By handling the technical heavy lifting, Tamarind empowers researchers to concentrate on their scientific questions and accelerate the pace of discovery.
Accelerating Discovery with PRODIGY on Tamarind bio
Integrating PRODIGY on a platform like Tamarind would allow researchers to:
Perform High-Throughput Screening: The speed of PRODIGY makes it ideal for analyzing a large number of structures, such as those produced by docking simulations. Researchers could use the platform to screen thousands of potential protein-protein interactions to identify the most promising candidates with the highest binding affinities.
Validate Computational Models: After predicting protein complex structures with tools like AlphaFold2, researchers can use PRODIGY on Tamarind to evaluate the binding affinity of the predicted models and identify the most likely native structure from a set of decoys.
How to Use PRODIGY on Tamarind Bio
To leverage PRODIGY's power, researchers can:
Access the Platform: Log in to the tamarind.bio website.
Select PRODIGY: From the list of available computational models, choose the PRODIGY tool.
Upload Complex Structures: Upload one or multiple protein complex structures in PDB format to the Tamarind.bio platform.
Specify Chains: Provide the chain identifiers for the interacting molecules.
Run Analysis: The platform handles the calculations, providing binding affinity predictions within minutes.
Analyze Results: Researchers can download a report with the predicted ΔG and Kd values, along with detailed interface analysis, to guide their protein engineering efforts.