Why?

I'm not entirely sure. Just thought it might make a decent project because I have an interest in cellular mechanisms. I may expand it to show other pathways as well, if it turns out to be useful.

There are plenty of rough edges in it, especially in the animation (and that may be an understatement) but I wanted to share it at this stage anyway because some insight might be helpful. I do not have any real life sciences background, so there are some things I would not be able to gauge:

• I guess the most important thing to find out is whether it makes sense to look at, i.e. is it clear at first glance, and is the layout logical?
• Secondly, is the level of detail here useful and consistent (any areas of over- or under-detailing relative to the rest of it)?
• And of course, does such a thing make sense to have? Would it actually be helpful in any scenario, or at the very least be a decent demonstration?
  

It is live on GitHub pages https://blowncapacitor1.github.io/MetabolismSimulator/ if you'd like to see it.

(Yes, I know the code is terrible. I have already posted it on r/ programminghorror)

You don't have to answer these questions specifically. I would really appreciate any feedback of any kind.

Thanks.

^{Just for the record, I did not use AI to make the graphics, do research for me, or write this post. The code is half AI, but would have been more had I not wasted my copilot credits doing dumb things like making it change my desktop wallpaper.}

My worksheet tells me that Histidine has pKa of 6.6 in oxygenated form, and 8.2 in deoxygenated form. I'm now trying to understand how this is beneficial, and link this to my understanding of bicarbonate buffer system in RBC and Bohr Shifts Ideas.

Any help appreciated!

My thinking so far:

For deoxy, lets imagine there is lot of muscle cell respiration. so lots of carbonic acid formation and dissociation, pH decreases. With deoxy Hb with histidine (pka 8.2), this would cause the deoxy Hb to pick up the protons.

This causes more carbonic acid dissociation (as equilibrium shifts)- the lower pH causes Hb affinity for oxygen to decrease, so more oxygen provided to respiring muscle cells.

I think my logic makes sense. But how does this link for Oxy Hb (with histidine pka 6.6)?

The frustrating part is that I understand the process in theory, but I am not familiar with the software so it takes me forever. I am currently having difficulties with 2 things:

1. Molecular Replacement gives me a solution where the peptide is broken, so Coot reads it as 2 chains rather than one. Why does this happen since a sequence was given? Can it be fixed?
2. I have to modify a residue and I can import it using the 3 letter code but Coot places it in a conformation that doesn't make much sense, I want to flip it so that it goes on top of the electron density blob but I keep failing at this.

Are you aware of any resources, such as a mailing list or a forum, where one can ask questions and people can exchange information, about Coot or other protein crystallography programs? I have already read the Coot manual and checked their youtube channel but found no solution to my 2 problems.

EDIT: You are incredibly helpful, thank you so much. I will respond asap ( weekends are usually hectic for me). I am using Coot 0.9, ccp4i2, Molrep, and Refmac5. I would like to use Phenix but I don’t have a Mac and it keeps crashing on PC.

Have you read a cool paper recently that you want to discuss?

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Have you recently published something you want to brag on?

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I made a 13-minute introduction to cancer evolution, and the imatinib section may be of interest here. It connects a molecular change in a drug target with selection among cancer-cell populations.

In Gorre et al. (2001), resistance was associated with a threonine-to-isoleucine substitution in the ABL kinase domain in six of nine patients; the other three showed BCR-ABL amplification. So the example involves both altered drug-target interaction and increased gene copy number, rather than one universal resistance mechanism.

Original paper: https://pubmed.ncbi.nlm.nih.gov/11423618/

The imatinib section starts at 8:55. The broader video uses melanoma to introduce clonal diversity and then discusses TRACERx and experimental adaptive therapy. I'm a genetics PhD at UCL studying cancer evolution; the video description includes references and corrections to the simplified narration.

I’m a second-year biochemistry student in Chile, and my university focuses heavily on the academic side of the field. Many people in my country have told me that the environment in Chile is terrible—really bad—but I’m very passionate about biology, and especially chemistry—the sciences in general. I’d love to hear the perspective of people from outside—what it’s like to be a biochemist, what your own experiences have been, maybe some advice? Tell me a bit about it!.

(I used a translator for this—I speak Spanish, but I didn’t feel like writing it all out in English myself, and it’s a bit of a struggle for me!)

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

Hi, I'm a student and I made a game to learn the 20 standard amino acids.

It works like Pokémon. You explore a cell, and to catch an amino acid you have to recognize its structure. The ones you get wrong show up more often until you learn them. You also learn the 3- and 1-letter codes, charge, pKa values, pI, hydropathy and codons.

It's free and open source. It runs in the terminal on Windows, macOS and Linux. It's in English and Spanish.

It's still in development, so I'd like feedback, especially if any value or structure is wrong. The values are from Lehninger at 25 °C.

https://github.com/leomorgzzz/aminomon

Hi, I need to dissolve pepsin, either in di water or in 0,1 M HCl. But I always get a cloudy solution, with sediment after some time of sitting on the shelf. Is it normal? Articles don't mention anything specific about the process, they don't even mention activity of pepsin.

Have you read a cool paper recently that you want to discuss?

Do you have a paper that's been in your in your "to read" pile that you think other people might be interested in?

Have you recently published something you want to brag on?

Share them here and get the discussion started!

Hi everyone,

As you know from the title, I'm trying to find opportunities to research in the field of biochemistry and want to get a headstart in the field of research. I am that kind of person who never took AP Biology or other advanced biology courses because my counselor focused on credit completion to meet the prerequisite for high school graduation. Therefore, I am more of a layman in the field of biology but plan to take premed. I always had the passion to delve into places where technology and science overlap.

However, I don't know where to start from. I have downloaded PyMol and started learning it to make my resume valuable while cold-emailing professors .

Do you guys have any tips for me. =]

Zotero Plugin: https://github.com/MOMISBACK/ProtPeek/tree/main/zotero

Chrome: https://chromewebstore.google.com/detail/mjiidagjpbabdncmgpabcijgndnbemck?utm_source=item-share-cb

Firefox: https://addons.mozilla.org/fr/firefox/addon/protpeek/

I am a biochem major currently in my biochem 2 lecture all about metabolism, pathways, regulation. What is the best way to master the lecture and its contents. My professor has a habit of asking things in a weird way and he says if you have mastered the content you can answer in any direction or explain deep dive. I would appreciate any advise I can get. Thank you.

Studying biochemistry for my undergraduate bachelor's degree, honestly wasn't expecting it to be so humbling. For example this week we are looking flagellum motors and honestly it just leaves me speechless. This subject has given me so much appreciation for life and helped me grow and mature. The slow understanding of the connectedness of all biotic processes on earth really gives you a completely different perspective. Yes I have my struggles and it is difficult, but I love it so so much.

We built an automated workflow that converts molecular docking results into validation-driven scientific videos.

This example uses AutoDock Vina to predict the binding mode of Ensitrelvir (Xocova®) against SARS-CoV-2 Main Protease (Mpro). The top-ranked pose was validated against the experimental structure, yielding an RMSD of 1.2 Å.

The entire video, including molecular visualizations, validation scenes, annotations, and sequencing, was generated automatically from the docking results. No manual animation was used.

Feedback is welcome.

I'm an undergrad student who's taking o chem 2 right now and I find it really interesting. I love learning about mechanisms and the concept of it is just really fun. However, I've been thinking of doing a biochemistry minor, but I honestly don't know anything about it nor do I know if I'm going to like it. So what's learning biochemistry like? Is it really memorization heavy like biology or is it process oriented like o chem or physiology?

Trying to decide what classes to take?

Want to know what the job outlook is with a biochemistry degree?

Trying to figure out where to go for graduate school, or where to get started?

Ask those questions here.

i'm trying to see where a mini unit on electrophoresis would fit into a chemistry teacher i'm helping's current lesson plans, so if someone could help me see where it would fit into this list, i'd much appreciate it:

• compounds, names, formulas
• modern atomic model
• chemical bonding and molecular shape
• mole
• chemical reactions
• stoichiometry
• gases and gas laws
• solids, liquids, and intermolecular forces
• thermochemistry
• solutions
• kinetics and equillibrium
• acids and bases
• solution equilibrium
• thermodynamics
• electrochemistry
• nuclear chemistry and radiation

i was thinking intermolecular forces and possibly chemical bonding, but i don't really know how much those fit; since electrophoresis is the physical movement of molecules, i was going to say kinetics, but it doesn't really involve equilibrium at all.

My (26M) familliy has a big firm which sells supplements nationwide. I’ve been working there for 2 years and my knowledge in supplements and in selling skills are good. I find it very interesting and I even thought going to uni for a biochemistry degree. The problem is it would last 4 years and would cost a very decent amount of money. With that in mind I figured I don’t necesseraly need to go to uni for it I just want to expand my knowledge so I could be an even better salesman. Do you guys have some tips as in what literature I could read, some basics I should educate myself on first, etc… Thanks in advance!

I’m a high school student in my final year, and I want to study biochemistry but everybody around me says that I should go into the medicine field and are saying that I would never find a stable career with it, is it true?

Hi all! I'm a physicist turned biochemist and I'm taking a biochem class for my masters. For one of our assignments, we are given a protein complex and need to write an essay describing how the structure might inform its function. From the research I've done so far, it seems very similar to a transcription regulator protein (has several alpha-helices and 2 beta sheets); if I open the protein complex file in PyMOL, there is also a chunk of DNA very close to the protein. However, I can also see 2 lone atoms in the structure - Zinc and Nickel. From what I've gathered, Zinc might be a stabilizer for the structure, but I'm not exactly sure what the Nickel does. I would love some direction/insight into how these atoms are utilized in proteins generally - I'm trying to avoid using AI and thought this sub might be a good resource in case someone here has specific experience with a protein like this. Happy to provide more details also! PS the protein looks very similar to 1HEW protein in structure, but with no NAGs (it's just the single chain and 2 atoms).

I'm a bsc biochemistry, 2nd year student currently looking for winter internship opportunities preferably in Kolkata.

Field: Biological sciences

Did anyone do anything similar? And what's the process of applying? I want to do a research based program. If possible, under Calcutta University.

Have you read a cool paper recently that you want to discuss?

Do you have a paper that's been in your in your "to read" pile that you think other people might be interested in?

Have you recently published something you want to brag on?

Share them here and get the discussion started!