Use Prodigy Binding Affinity Prediction

Official Neurosnap webserver for accessing Prodigy Binding Affinity Prediction online.

Drug Discovery

Overview

PRODIGY (PROtein binDIng enerGY prediction) is a computational tool for predicting the binding affinity of proteinā€“protein complexes using their 3D structures. Leveraging an efficient contact-based approach, PRODIGY estimates binding free energy and dissociation constants while providing insights into structural determinants of protein interactions. By combining interfacial contact properties with non-interacting surface features, PRODIGY delivers reliable predictions critical for understanding molecular interactions, guiding therapeutic development, and engineering protein complexes.

Neurosnap Overview

The Prodigy Binding Affinity Prediction online webserver allows anybody with a Neurosnap account to run and access Prodigy Binding Affinity Prediction, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Accepts 3D structural input of proteinā€“protein complexes in PDB format.
  • Calculates binding free energy (āˆ†G) and dissociation constant (Kd) based on interfacial contact analysis.
  • Provides a detailed report, including the number and type of intermolecular contacts, percentage of charged and polar residues, and residue-specific interactions.

Statistics

Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.

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API Request

Access Prodigy Binding Affinity Prediction using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.

Job Note

Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.

Configuration & Options

Service Inputs

The input PDB to analyze.

Distance cutoff to calculate intermolecular contacts. Note: you can leave this as is to use the default.

Accessibility threshold for BSA analysis. This parameter defines the minimum surface area accessibility required to consider a region as part of the binding interface during analysis. It is used to refine the calculation of buried surface area (BSA), which is critical for evaluating interaction interfaces. Note: You can leave this parameter as is to use the default threshold set by the program.

The temperature for calculating the dissociation constant (Kd). Note: you can leave this as is to use the default value of 25Ā°C.

Provide the chain identifier(s) for the first molecule involved in the interaction. For molecules spanning multiple chains, use a comma-separated format (e.g., A,B). Note: If this is left empty, Interactor 2 must also be left empty. By default, all intermolecular contacts are taken into consideration when both are empty.

Provide the chain identifier(s) for the second molecule involved in the interaction. For multiple chains, use a comma-separated format (e.g., X,Y,Z). Note: If this is left empty, Interactor 1 must also be left empty. By default, all intermolecular contacts are taken into consideration when both are empty.

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