Events 2018-2019

[pikachu4919]

You are mistaken. Magnetism has been in the rules in the past and will likely be in the rules again this year.

And this is why I stay in bio and chem events instead of dabbling in physics ones (with the exception of thermo, I guess....but thermo is important to all fields of engineering so nonetheless I know it anyways )

Yes go back to the bio and chem event forums, this is my territory

Protein Modeling event actually also has its own Facebook page

Wow I had no idea about this and just looked it up and its actually incredible that it exists. Being able to see what the TOP TEAMS IN THE NATION did for their prebuild regarding material and design is a HUGE advantage for all the users that see this post on this site.

And you having no idea about it is exactly why the bio and chem events are my territory, windu. Have fun in physics!

In all seriousness tho, yes, it is definitely a great resource for model inspiration.

[luanne]

YALL:
any tips on how to study for protein modeling??
anything appreciated

[I placed 10th at nats in this event in 2016, thus I know what I'm talking about]

The CBM MSOE website should have everything you need to know, although I'd also suggest looking into additional sources for general protein biochemistry information. I definitely advise that you don't forget about the exam, but that you also remember to put lots of energy into building your prebuild model and practicing with jmol in prep for onsite. Those two models are worth 70 percent of your score, and your exam is only worth 30 percent. If you want to see examples of models, see some of the Best of Nationals wikis (particularly 2015/2016 or 2011/2012, as those were the last two pairs of years when protein was run), and the Protein Modeling event actually also has its own Facebook page, where it has posted photos of competitors with models that they brought to be judged for the 2016 National Tournament, which was the most recent year when protein was run.

Hope this is a good enough amount of info to get you started.

thanks so much!
but what do you mean by "practicing with jmol"
sorry I am completely new to this and usually compete in materials sci but it got thrown out ;/

[bernard]

YALL:
any tips on how to study for protein modeling??
anything appreciated

[I placed 10th at nats in this event in 2016, thus I know what I'm talking about]

The CBM MSOE website should have everything you need to know, although I'd also suggest looking into additional sources for general protein biochemistry information. I definitely advise that you don't forget about the exam, but that you also remember to put lots of energy into building your prebuild model and practicing with jmol in prep for onsite. Those two models are worth 70 percent of your score, and your exam is only worth 30 percent. If you want to see examples of models, see some of the Best of Nationals wikis (particularly 2015/2016 or 2011/2012, as those were the last two pairs of years when protein was run), and the Protein Modeling event actually also has its own Facebook page, where it has posted photos of competitors with models that they brought to be judged for the 2016 National Tournament, which was the most recent year when protein was run.

Hope this is a good enough amount of info to get you started.

thanks so much!
but what do you mean by "practicing with jmol"
sorry I am completely new to this and usually compete in materials sci but it got thrown out ;/

Jmol is a tool used to view, study, and annotate protein structures on a computer. You can download files with protein structures from databases and open them in Jmol. In past years, a "pre-build model" was specified in the rules for you to create a physical model before coming to the competition and you would create a physical model at the competition of an "on-site model" that was different for each level of competition. Being comfortable with the operations available in Jmol is helpful for that process.

[luanne]

Jmol is a tool used to view, study, and annotate protein structures on a computer. You can download files with protein structures from databases and open them in Jmol. In past years, a "pre-build model" was specified in the rules for you to create a physical model before coming to the competition and you would create a physical model at the competition of an "on-site model" that was different for each level of competition. Being comfortable with the operations available in Jmol is helpful for that process.

Also, do you have any suggestions what textbook to use when studying for the test portion of this event?

[bernard]

Jmol is a tool used to view, study, and annotate protein structures on a computer. You can download files with protein structures from databases and open them in Jmol. In past years, a "pre-build model" was specified in the rules for you to create a physical model before coming to the competition and you would create a physical model at the competition of an "on-site model" that was different for each level of competition. Being comfortable with the operations available in Jmol is helpful for that process.

Also, do you have any suggestions what textbook to use when studying for the test portion of this event?

I haven't competed in the event, only helped with the pre-build part so I can't give any specific textbook recommendations. I think you could start by reading the chapters on biological macromolecules (structure and function) and the central dogma in a general biology textbook. Before rules are published, you can research sample proteins and open their structures in Jmol to get a feel for what proteins may do and how structure may affect their interactions. In September after rules are published you'll want to learn about the topic for the year and proteins relevant to that topic. I think you may find some topics too new to be explained in depth in a textbook.

MSOE Center of BioMolecular Engineering, a sponsor for the event, has a webpage for the event. It'll be helpful for getting a better idea of the event but may not be updated with 2018-2019 details until after rules are published.

[pikachu4919]

Jmol is a tool used to view, study, and annotate protein structures on a computer. You can download files with protein structures from databases and open them in Jmol. In past years, a "pre-build model" was specified in the rules for you to create a physical model before coming to the competition and you would create a physical model at the competition of an "on-site model" that was different for each level of competition. Being comfortable with the operations available in Jmol is helpful for that process.

Also, do you have any suggestions what textbook to use when studying for the test portion of this event?

I haven't competed in the event, only helped with the pre-build part so I can't give any specific textbook recommendations. I think you could start by reading the chapters on biological macromolecules (structure and function) and the central dogma in a general biology textbook. Before rules are published, you can research sample proteins and open their structures in Jmol to get a feel for what proteins may do and how structure may affect their interactions. In September after rules are published you'll want to learn about the topic for the year and proteins relevant to that topic. I think you may find some topics too new to be explained in depth in a textbook.

MSOE Center of BioMolecular Engineering, a sponsor for the event, has a webpage for the event. It'll be helpful for getting a better idea of the event but may not be updated with 2018-2019 details until after rules are published.

I don't think I've really used a textbook that much for this event. Most points come from your models (prebuild and onsite), and even then, MSOE's exams focus more on the topic protein of the season more than general protein biochemistry itself. Even then, in my honest opinion, most of that general biochemistry is probably at 9th grade honors bio level. Some of it may reach AP bio level difficulty, but it's never that hard, and a lot of the concepts can be covered by study of the proteins of the theme. That's just me, tho.

[windu34]

Also, do you have any suggestions what textbook to use when studying for the test portion of this event?

I haven't competed in the event, only helped with the pre-build part so I can't give any specific textbook recommendations. I think you could start by reading the chapters on biological macromolecules (structure and function) and the central dogma in a general biology textbook. Before rules are published, you can research sample proteins and open their structures in Jmol to get a feel for what proteins may do and how structure may affect their interactions. In September after rules are published you'll want to learn about the topic for the year and proteins relevant to that topic. I think you may find some topics too new to be explained in depth in a textbook.

MSOE Center of BioMolecular Engineering, a sponsor for the event, has a webpage for the event. It'll be helpful for getting a better idea of the event but may not be updated with 2018-2019 details until after rules are published.

I don't think I've really used a textbook that much for this event. Most points come from your models (prebuild and onsite), and even then, MSOE's exams focus more on the topic protein of the season more than general protein biochemistry itself. Even then, in my honest opinion, most of that general biochemistry is probably at 9th grade honors bio level. Some of it may reach AP bio level difficulty, but it's never that hard, and a lot of the concepts can be covered by study of the proteins of the theme. That's just me, tho.

I didn't do this event, but it was three of my friends that placed 2nd at Nats in 2016 and I observed a decent amount of their prep. As Pika said, the general protein biochem didn't seem to be the biggest concern, but rather my teammates spent alot of time reading papers on the topic protein and gaining an incredible understanding of it and its applications. Of course, the prebuild and on-site build are arguably more important and at least one of the competitors should be completely dedicated to mastering the prebuild and onsite build (practice!!!)

[luanne]

YALL:
any tips on how to study for protein modeling??
anything appreciated

[I placed 10th at nats in this event in 2016, thus I know what I'm talking about]

The CBM MSOE website should have everything you need to know, although I'd also suggest looking into additional sources for general protein biochemistry information. I definitely advise that you don't forget about the exam, but that you also remember to put lots of energy into building your prebuild model and practicing with jmol in prep for onsite. Those two models are worth 70 percent of your score, and your exam is only worth 30 percent. If you want to see examples of models, see some of the Best of Nationals wikis (particularly 2015/2016 or 2011/2012, as those were the last two pairs of years when protein was run), and the Protein Modeling event actually also has its own Facebook page, where it has posted photos of competitors with models that they brought to be judged for the 2016 National Tournament, which was the most recent year when protein was run.

Hope this is a good enough amount of info to get you started.

I didn't do this event, but it was three of my friends that placed 2nd at Nats in 2016 and I observed a decent amount of their prep. As Pika said, the general protein biochem didn't seem to be the biggest concern, but rather my teammates spent alot of time reading papers on the topic protein and gaining an incredible understanding of it and its applications. Of course, the prebuild and on-site build are arguably more important and at least one of the competitors should be completely dedicated to mastering the prebuild and onsite build (practice!!!)

So i'm playing around with jmol and using the practice on-site from 2018 "1js3.pdb".. I pretty much figured the functions out but i need to represent amino acids 253-317 of chain a. I typed into jmol "select 253-317" and i got the output 1056 atoms selected.
Am I doing this correctly? If so, how am i suppose to fold the mini-toober....

[EastStroudsburg13]

Yep, that's correct. Keep in mind that each amino acid is a molecule that has quite a few atoms, and with your toober you are only folding based on the amino acid chain. If there are specific atoms important to the structure of the protein, such as the sulfur atoms of cysteines involved in a disulfide bond, those may be worth modeling, but nobody expects you to model every atom.

[pikachu4919]

YALL:
any tips on how to study for protein modeling??
anything appreciated

[I placed 10th at nats in this event in 2016, thus I know what I'm talking about]

The CBM MSOE website should have everything you need to know, although I'd also suggest looking into additional sources for general protein biochemistry information. I definitely advise that you don't forget about the exam, but that you also remember to put lots of energy into building your prebuild model and practicing with jmol in prep for onsite. Those two models are worth 70 percent of your score, and your exam is only worth 30 percent. If you want to see examples of models, see some of the Best of Nationals wikis (particularly 2015/2016 or 2011/2012, as those were the last two pairs of years when protein was run), and the Protein Modeling event actually also has its own Facebook page, where it has posted photos of competitors with models that they brought to be judged for the 2016 National Tournament, which was the most recent year when protein was run.

Hope this is a good enough amount of info to get you started.

I didn't do this event, but it was three of my friends that placed 2nd at Nats in 2016 and I observed a decent amount of their prep. As Pika said, the general protein biochem didn't seem to be the biggest concern, but rather my teammates spent alot of time reading papers on the topic protein and gaining an incredible understanding of it and its applications. Of course, the prebuild and on-site build are arguably more important and at least one of the competitors should be completely dedicated to mastering the prebuild and onsite build (practice!!!)

So i'm playing around with jmol and using the practice on-site from 2018 "1js3.pdb".. I pretty much figured the functions out but i need to represent amino acids 253-317 of chain a. I typed into jmol "select 253-317" and i got the output 1056 atoms selected.
Am I doing this correctly? If so, how am i suppose to fold the mini-toober....

Yep, that's correct. Keep in mind that each amino acid is a molecule that has quite a few atoms, and with your toober you are only folding based on the amino acid chain. If there are specific atoms important to the structure of the protein, such as the sulfur atoms of cysteines involved in a disulfide bond, those may be worth modeling, but nobody expects you to model every atom.

Yes, your mini toober represents the amino acid backbone, and you rarely need to show individual atoms. Additionally, when you use the select command, it’ll do only that. If you want to make only that part of the protein visible while cutting out everything else from your interface, use restrict 253-317 instead. However, it definitely does help to select before restrict if you’re unsure since I believe the online Jsmol servers used in competition don’t really let you undo any commands, hence you have to be quite careful with using the restrict command.