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I am new to the field of molecular biology. I am finding the need to generate illustrative figures displaying interplay between proteins, DNA and various other molecular constructs at different scales of complexity and having trouble identifying tools that many use to generate their very descriptive figures. For example there are countless examples of DNA and wrapped around histones, in 2D, in 3D, in almost realistic rendered versions etc. Obviously, I can not use someone else's graphics - so I am curious where do others start? Any advice on best practices would be greatly appreciated there, in terms of tools people use to generate their molecular biology figures describing biological 3D mechanistic illustrations.

Below are 4 classes of illustrations that I have found on the web and I am including here only for the purpose of example of each type:

Type 1 has actual 3d components (histones) and DNA wrapped around for example: it's not clear if these are made in some kind of a 3D program, or they are 2D constructs somehow manipulated and put together with some clever efforts. Are there specific 3D rendering or publishing tools/programs used for these? Perhaps one's with a library elementary blocks, somewhat akin to open-source 3D floor-map design programs many use to quickly create floor plans for their houses and apartments furnished with 3D chairs, tables and other furnishings?

Type 2: These tend to be 3D rendered constructs, like the simplified version of the chromatin ball here. Some are very realistic, and I can imagine those are done professionally by studios, and not biologists, but simpler versions like this one should be possible without a professional studio's help.

Type 3: This is more like old school hand drawn illustrations. These days, perhaps there are tools to do this with library of 2D elements that can be manipulated and placed in to create this type of illustrations?

Type 4: This type uses simpler 2D elements that are put together to create more complex biological constructs, like cells, cellular activity etc. This type is less helpful in capturing 3D interplay and relationships between DNA and proteins but still a tool with library of objects that could be morphed to fit into the right shape(s) would be helpful.

Thank you. enter image description here

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    $\begingroup$ Actually, you probably can use someone else's graphics, provided you obtain a license. There are many stock photo and illustration companies, and if none of the existing images match your needs, you can always commission a scientific graphic artist to produce illustrations to your specifications. $\endgroup$
    – MattDMo
    Commented May 14, 2023 at 19:23
  • $\begingroup$ Welcome to Biology StackExchange! Can you please give an example or two of such figures so that we can give you more concrete guidances? $\endgroup$
    – Domen
    Commented May 14, 2023 at 21:07
  • $\begingroup$ Thank you @Domen, I have included a few examples. $\endgroup$
    – Zebra Fish
    Commented May 14, 2023 at 23:30
  • $\begingroup$ Figures 1 and 3 were drawn by professional artists, probably using Adobe Illustrator — Figure 4 probably also, but the nearest thing to that I am aware of is BioRender, as mentioned in a previous post in this general area. Any 3D proteins graphic program will output diagrams of type 2, but you need to know how to get the style and colour of picture you need. There is a learning curve. $\endgroup$
    – David
    Commented May 15, 2023 at 12:29
  • $\begingroup$ Thank you very much @David, BioRender appears to top the list. $\endgroup$
    – Zebra Fish
    Commented May 16, 2023 at 3:33

1 Answer 1

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Stick with „vector graphic design“ applications. They enable you to open .pdfs and move around individual elements and resize them to your needs without losing resolution.

  1. Biorender. It has a lot of ready-to use illustrations of proteins, organelles, receptors, etc. Free subscription is very limited, though. I don‘t have a lot of experience with it, but it might be the best solution for every molecular biologists. It‘s worth asking your professor if he buys one license for the whole group. Everyone loves biorender figures.
  2. Adobe illustrator. Best vector graphic design software out there. But expensive as hell and takes a few days to learn.
  3. Affinity publisher (My favorite!). Perfect for making posters and publication grade figures. You pay 50 bucks once and own the license forever. It‘s powerful and has more than enough features to make top-notch professional figures. Adobe illustrator is better though. Affinity publisher also takes a few days to learn.
  4. Inkscape. Open source 100% free vector graphics. Haven‘t used it a lot, but might be a good entry point.
  5. Microsoft powerpoint. It‘s bad, but it gets the job done in terms of placing objects next to each other. But I made big complex posters with it that look alright.
  6. Apple Keynote. Like powerpoint but a lot better and a lot more precise. Only for mac users, though

For 3D rendering protein structures, I recommend pymol. Every structural project probably used pymol at some point. I have seen people even script some fancy animations with it, it takes some python scripting, though.

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