3D protein visualization tools

Published on 02/5/2023 by Jose Cancino ‐ 4 min
3D protein visualization tools

A protein structure or more specific the three-dimensional arrangement of atoms in a protein molecule, determines how the protein interacts with other molecules in the cell and how it carries out its biological functions.

Online tools for 3D protein visualization

The Protein Data Bank (PDB) is a database that provides access to structural data of large biological molecules such as proteins and nucleic acids for free. It is considered as a valuable resource for researchers in the field of structural biology.

PDB enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of these data in context of external annotations providing a structural view of biology.

A Computed Structure Model (CSM) is a protein structure model generated using computational methods such as homology modeling or ab initio modeling. These models are created based on the sequence of the protein and other available structural information.

CSM can be useful when the experimental structures are not available or when the experimental structures are of low resolution. RCSB PDB integrates PDB with CSM data from AlphaFold, making it the most extensive site to render 3D protein structures online (Image 1).

The RCSB  Protein Data Bank

Image 1. The RCSB Protein Data Bank 3D visualization screen.

A popular CSM software is AlphaFold, a deep learning-based protein structure prediction algorythm developed by the DeepMind team. All of its data is freely available for both academic and commercial use under a CC-BY 4.0 license. The software is highly accurate in predicting protein structures; it uses a neural network to predict the 3D structure of a protein from its amino acid sequence.

It provides over 200 million protein structure predictions. Only in 2021, a collaboration between the European Molecular Biology Laboratory and DeepMind has predicted structures for over 350,000 proteins for 21 model organisms.

UniProt is a core data resource that provides a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. It is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR).

It contains a large amount of information on the biological function of proteins derived from the research literature, including information on protein-protein interactions, subcellular locations, disease associations, post-translational modifications, and more.

Molecular visualization softwares (MVS)

PyMOL, Chimera, VMD, Jmol and Blender are MVS that can be used to render computed structure models of proteins. These software provide a range of features such as rendering of high-quality images and videos, analysis of protein-ligand interactions, and more.

You can download the structure file of the protein you want to render from databases (RCSB PDB, AlphaFold, etc.) or other online tools and then load it into the software of your choice. Once you have loaded the structure file, you can use the software’s tools to manipulate and visualize the protein structure (Image 2).

Blender dashboard

Image 2. Visualization of a protein 3D structure in Blender.

A special mention is for Blender, a free and open-source 3D creation software that supports the entirety of the 3D pipeline modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing. It has a comprehensive array of modeling tools that make creating, transforming and editing models easy.

Blender’s modeling toolset is extensive and includes full N-Gon support, edge slide, inset, grid and bridge fill, advanced sculpting tools and brushes, multi-resolution and dynamic subdivision, 3D painting with textured brushes and masking. Blender also has a high-end production path tracer called Cycles that allows you to create jaw-dropping renders.

The choice between Blender, PyMOL, Chimera, VMD or Jmol depends on your specific needs and preferences. PyMOL is often preferred for viewing and creating publication-quality images. VMD is also a popular choice for analyzing the results of molecular dynamics simulations. Chimera is also useful for interactive homology modeling.

The Blender plugin BlendMol is capable of importing VMD or PyMOL scenes into Blender and can be used to create enhanced images for use in journals, outreach programs, websites and classes.

It’s important to try out these tools and see which one fits all your needs. Most of the time more than one tool will be used, since there is no single software that contains all the features.

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