Structure prediction & homology modelling
12 important questions on Structure prediction & homology modelling
Explain how the concept “Structure is more conserved than sequence” is used.
Give the 4 steps of homology modelling.
- Find a template
- Make an alignment between your sequence and the template
- Create a homology model (modeller)
- loop modelling
- rotameroptimisation
- Validate your structure
What is threading/fold recognition?
- Fit your sequence onto existing structures (may not indicate homology):
- We need a score to evaluate how well a sequence fits onto a structure
- we use a “potential”
- Note that threading is effectively an alignment problem between a sequence and a structure: Gaps may be introduced
- Higher grades + faster learning
- Never study anything twice
- 100% sure, 100% understanding
For my 1st exam I got a C. Then, I started looking for ways to learn better and I came across Study Smart. Since then I have scored a A+, A, A- and another A. I highly recommend it to everyone who wants to hear it. I am so happy with it!!
I was struggling to finish all my first-year subjects for 3 years. Then I discovered Study Smart, which helped me to finish all of them within 3 months.
Because of StudySmart, things are going well in many ways. Before, I always had study stress and no time for anything. Now I feel calm and confident (because of the program). I used to score a B, now I usually score an A or A+.
Hey Chris, I really want to thank you very much for developing the platform, I usually got around C for my exams, now I scored an A+, an A and a A- !!
Since using Study Smart, my average has increased significantly. I even completed a statistics course with a A+ while I'm bad at statistics. I took on extra courses this year, because of Study Smart. Thanks so much!
Ever since I started studying with StudySmart I passed all my exams !!! No more re-sits!! At first, I was happy with a pass and now I only get good grades. Many thanks!
I aced all the courses I studied with Study Smart. For law, I first scored a D, and now an A! I’m 100% sure that I’ll pass all the courses I study with Study Smart.
I always thought I studied well. My grades were fine. I could never have imagined that applying these study skills would have such a huge and direct impact on my grades, my speed and the pleasure I have in learning.
For the first time, I finally feel totally confident about the way I learn. I have the perfect overview and make great progress in terms of speed and the grades I get. Thanks, Chris!
I immediately started to enjoy learning again, and my grades soared. All of a sudden, everything went better. I highly recommend Study Smart to all students..
Being able to create my materials online made the process of studying so much smoother and quicker. I no longer have to spend a huge amount of my time on creating my summaries.
At first, my notes were a mess. Now I use Study Smart to take my notes in a perfectly structured way. It helps me to save a lot of time and do other things I enjoy.
Students that study with Study Smart get better grades. The system applies all the learning methods in such a way that both well-performing students and students who struggle perform much better.
Hi Chris, I would like to thank you very much. Last year I scored C on a course, and this year I got an A+ thanks to your method! Thank you very much!
The largest effect is that my child is more enthusiastic about school! Every parent wants their children to be happy at school, Study Smart made it happen.
In high school, I failed several exams, and that has really changed now. I actually needed this tool very much back then. Since I started studying with StudySmart, I haven't had any D's. My average score is now an A and those are results I would have never had in the past
With my old method, I passed only 3 out of 8 courses. Since I started taking my notes digitally in Study Smart, I have passed all my courses on the first try. For me, StudySmart takes away the stress of wondering if I will pass or not.
Thanks to StudySmart, I passed all my exams, and with better grades than before! On top of that, I have mastered a very good study method now, which I am confident will help me earn my degree.
What is a pairwise residue contact potential?
- Gives an energy between two residues
- Can be calculated by considering the contacts of a residue
- A contact is a pair of residues that are close in 3D space
- Two hydrophobics would give a low energy in such a potential (they are favourable)
When creating an alignment, what to look out for?
- Is anything about the function of the target & template known?
- Can we recognise any functional motifs? –align by hand!(or Motif Aware Praline)
- general: MSA of profile alignment
What are the constraints in MODELLER based on?
What is simulated annealing?
- Simulated using the constraints and knowledge based potential (simulated as E)
- Lower the temperature (T) during the simulation (constraints and potential become more important)
- This is a way to minimize the energy (potential) of a system
(entropy is left out)
What is done for structure refinement?
How are all models by modeller evaluated and how can you pick the best one?
- (experimental structure validation)
- hydrogen bonds
- distances
- phi/psi angles
- for evaluating models:
- globularity (compactness)
- amount of secondary structure
- amount of hydrogen bonds
- protein "like" features
molprobity = good example
Meta-servers: what are ensemble methods?
How accurate is Secondary Structure Prediction?
- Secondary structure prediction is relatively accurate
- Predict secondary structure for your target sequence
- Compare to assigned structure for your (suggested) template
What is global distance test?
GDT_TS --> total score from global distance test.
why less sensitive to outliers?
The question on the page originate from the summary of the following study material:
- A unique study and practice tool
- Never study anything twice again
- Get the grades you hope for
- 100% sure, 100% understanding
