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BioBlender: Blender for Biologists

bioblender.eu

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Re: BioBlender: Blender for Biologists

#11

Post by archgoon »

car wrote: post #4

Does anyone know how to 3D-print protein structures?

You do not 3D-print protein structures (unless you mean 3D models of proteins in which case ignore the rest of this post). Not in the sense of "here's an arbitrary position of atoms, give me a molecule". There's a reason why Folding@Home takes a lot of processing power. It's very hard to figure out how chains of amino acids will interact with themselves.

The best you can do is do gene synthesis using a method called Oligonucleotide Synthesis

http://en.wikipedia.org/wiki/Oligonucleotide_synthesis

Using this technique, you can take an arbitrary gene sequence (ATGC sequence) and get a plasmid out of it. This will specify a sequence of amino acids that will fold into a protein. Then you just have to get a bacterial host to take it up into it's DNA and then make sure the chemical conditions of the host are right to generate your protein (you can't synthesize a protein if there aren't the right types of Amino Acids floating around, for example).

Companies like Genscript (which I found by randomly googling) will manufacture a specified gene, and send you back frozen plasmids, which you can then inject into your favorite bacterial host.

http://www.genscript.com/gene_synthesis.html

Re: BioBlender: Blender for Biologists

#12

Post by kayhi »

clarle wrote: post #6

Sounds really cool! We usually just use PyMOL [1] in our lab, but it looks like BioBlender takes PyMOL, Blender, and a few other structural biology and builds on top of both of them. It looks like the biggest contribution from BioBlender is that it takes properties such as electrostatic potential and combines it with Blender's physics engine to better simulate movement when creating molecular animations. Most of our…

Great to see some other crystallographers in the crowd, also worth checking out is Discovery Studio Visualizer.

Re: BioBlender: Blender for Biologists

#13

Post by archgoon »

clarle wrote: post #8
goldfeld wrote: post #7

I have been wanting to get into bioinformatics, but there's something I miss coming from webdev: the ability to create something over a few weeks. I don't mean I want to discover something new, and I'm not sure I'd want to get into research at all. I wanted to be able to experiment and see stuff show up on a screen related to the structures and formulas I'm learning. Some fun and practical, even if not very useful (g…

Rosalind [1] (previously posted on HN) is pretty good for something like a Project Euler for bioinformatics. The problems are pretty similar to the introductory computational biology course at my school for upper-year undergrads and first-year grad students. It's a really good way to get a good overview of the field, and what some of the problems have been already solved in bioinformatics. It's definitely best to com…

That is absolutely fantastic! Kudos to UCSD and Saint Petersburg Academic University for creating such an awesome educational resource! And thank you for pointing me to it!

Re: BioBlender: Blender for Biologists

#14

Post by michaelbuddy »

archgoon wrote: post #11
car wrote: post #4

Does anyone know how to 3D-print protein structures?

You do not 3D-print protein structures (unless you mean 3D models of proteins in which case ignore the rest of this post). Not in the sense of "here's an arbitrary position of atoms, give me a molecule". There's a reason why Folding@Home takes a lot of processing power. It's very hard to figure out how chains of amino acids will interact with themselves. The best you can do is do gene synthesis using a method called…

"will manufacture a specified gene, and send you back frozen plasmids, which you can then inject into your favorite bacterial host."

As a fan of the Bioshock series, I wasn't sure if you were trolling here or I'm just completely unaware of the current state of real biology.

Re: BioBlender: Blender for Biologists

#15

Post by archgoon »

michaelbuddy wrote: post #14
archgoon wrote: post #11

Earlier quoted context omitted.

You do not 3D-print protein structures (unless you mean 3D models of proteins in which case ignore the rest of this post). Not in the sense of "here's an arbitrary position of atoms, give me a molecule". There's a reason why Folding@Home takes a lot of processing power. It's very hard to figure out how chains of amino acids will interact with themselves. The best you can do is do gene synthesis using a method called…

"will manufacture a specified gene, and send you back frozen plasmids, which you can then inject into your favorite bacterial host." As a fan of the Bioshock series, I wasn't sure if you were trolling here or I'm just completely unaware of the current state of real biology.

Not trolling! Honest!

http://en.wikipedia.org/wiki/Plasmid#Vectors

Re: BioBlender: Blender for Biologists

#16

Post by thundara »

clarle wrote: post #6

Sounds really cool! We usually just use PyMOL [1] in our lab, but it looks like BioBlender takes PyMOL, Blender, and a few other structural biology and builds on top of both of them. It looks like the biggest contribution from BioBlender is that it takes properties such as electrostatic potential and combines it with Blender's physics engine to better simulate movement when creating molecular animations. Most of our…

What worth would the 3d simulations produced by Blender's physics engine be? I'd imagine that they wouldn't even compare to those produced by full MD simulations, which are already of debatable correctness depending on the size of the system, force field + parameters, time step, solvent, etc...

Re: BioBlender: Blender for Biologists

#18

Post by daniel-levin »

clarle wrote: post #8
goldfeld wrote: post #7

I have been wanting to get into bioinformatics, but there's something I miss coming from webdev: the ability to create something over a few weeks. I don't mean I want to discover something new, and I'm not sure I'd want to get into research at all. I wanted to be able to experiment and see stuff show up on a screen related to the structures and formulas I'm learning. Some fun and practical, even if not very useful (g…

Rosalind [1] (previously posted on HN) is pretty good for something like a Project Euler for bioinformatics. The problems are pretty similar to the introductory computational biology course at my school for upper-year undergrads and first-year grad students. It's a really good way to get a good overview of the field, and what some of the problems have been already solved in bioinformatics. It's definitely best to com…

+1 for this.

Rosalind is a great way of improving your knowledge of biology and CS. It is quite cool to see computer science and mathematics problems and techniques applied to bioinformatics.

Re: BioBlender: Blender for Biologists

#20

Post by pedrobeltrao »

clarle wrote: post #6

Sounds really cool! We usually just use PyMOL [1] in our lab, but it looks like BioBlender takes PyMOL, Blender, and a few other structural biology and builds on top of both of them. It looks like the biggest contribution from BioBlender is that it takes properties such as electrostatic potential and combines it with Blender's physics engine to better simulate movement when creating molecular animations. Most of our…

I agree with the need for better visualization tools in biology. There is an interesting group/project started at UCSF and headed by Graham Johnson (www.grahamjlab.org/). Some of these tools are still closer to art than science but I think it is really worth the investment. It is clear that these will help us think about biological objects.
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