Navigating Between BLAST and iCn3D

Navigating Between BLAST and iCn3D

Explore protein structures and sequences quickly and easily 

Have you ever come across an unfamiliar protein in your BLAST results? With the newly added ‘AlphaFold Structure’ link (Figure 1), you can now explore its structure as predicted by AlphaFold in iCn3D. The iCn3D Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool with interactive displays of 3D structure, 2D topology, 1D sequence and annotation 

Features & Benefits
  • Upload AlphaFold structures to iCn3D directly 
  • Use the structure search feature to find structures of interest 
  • Understand important features of the structures, such as disease-associated variations (ClinVar), genetic variations (dbSNP), or chemical modifications (PTM) 
  • Identify similarities and differences between AlphaFold predictions and experimentally determined structure 
  • Gain insights into the structural characteristics and properties of the molecules 
  • Use iCn3D in different platforms (Jupyter Notebook, Virtual Reality, and Augmented Reality) 
  • Easily integrate iCn3D using scripted workflows (node.js, python) to analyze large sets of structures 

Figure 1: BLAST search results (alignment tab) with new ‘AlphaFold Structure’ link and visualization of the structure as predicted by AlphaFold in iCn3D. 

See our previous post about AlphaFold structures and iCn3D for more information.   

Stay up to date

BLAST is a part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.  

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We want to hear from you! Try it out and let us know what you think. If you have questions or would like to provide feedback, please reach out to us at   


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