How to Use IntFold Online
Try IntFold
Commercially Available Online Web Server
IntFold: A Controllable Foundation Model for Biomolecular Structure Prediction
IntFold, a controllable foundation model for general and specialized biomolecular structure prediction that is able to predict a wide range of biological interactions with accuracy comparable to the state-of-the-art AlphaFold 3. IntFold is a significant advancement in computational biology, as it provides a powerful platform for tackling complex challenges from drug screening to protein design by offering both high accuracy and exceptional user control.
How IntFold Works
IntFold is a versatile model that is built on a Diffusion Block and a custom attention kernel. Its core functionality is based on a diffusion-based process that iteratively generates structure samples, which are then ranked by a confidence head to produce the final prediction.
Custom Attention Kernel: The model utilizes a custom attention kernel that provides high performance, enabling it to achieve state-of-the-art accuracy on a comprehensive benchmark of diverse biomolecular structures.
Controllable Design: IntFold is designed for specialized applications, offering exceptional user control through a framework of adapters. These adapters enable specialized downstream tasks such as Guided Folding, Target-Specific Modeling, and Affinity Prediction.
Target-Specific Adapters: For applications like structure-based drug design, where capturing subtle conformational states is crucial, IntFold can be fine-tuned with a Low-Rank Adaptation (LoRA) architecture. This approach adds a small number of trainable parameters to the base model, allowing it to accurately predict inhibitor-induced structural shifts for specific protein families, such as the kinase family.
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 IntFold on Tamarind Bio
Using IntFold on a platform like Tamarind Bio would empower researchers to accelerate drug screening and protein design by:
Accurate Structure Prediction: Researchers could use IntFold to get accurate predictions for a wide range of biomolecular interactions, from proteins and nucleic acids to small molecules and ions. This capability is essential for understanding complex biological mechanisms.
Target-Specific Modeling: The platform could leverage IntFold's fine-tuning capabilities to create models that specialize in capturing rare conformational states for specific protein families, a significant hurdle for effective structure-based drug design.
High-Throughput and Automation: By integrating IntFold's computationally efficient model into a no-code platform, Tamarind would enable researchers to run large-scale prediction and design campaigns and rapidly generate high-quality candidates for further analysis.
How to Use IntFold on Tamarind Bio
To leverage IntFold's power, a researcher could follow this streamlined workflow:
Access the Platform: Begin by logging in to the tamarind.bio website.
Select IntFold: From the list of available computational models, choose the IntFold tool.
Select a Task: Choose a specific task, such as general structure prediction or a specialized task like guided folding or affinity prediction.
Provide Inputs: Provide the protein sequence and, for specialized tasks, additional inputs like structural constraints for known binding pockets or epitopes.
Run the Model: The platform would run the IntFold model, which would use its Diffusion Block to iteratively generate and rank structure samples.
Analyze and Refine: The final prediction would include confidence scores (pLDDT, pTM) to help you evaluate the quality of the model. You can use the predicted structure to guide further analysis and design efforts.