How to mutate protein computationally in Pymol (mutagenesis)

[@engr.muhammadzafar]

Dear Doctor Sahib, Excellent briefing and explaining is very buseful thanks

[@ridaayubch2814]

MASHALLAH, Your videos are very helpful for the beginners having little command over softwares and your passion for working in different areas also motivate others to look this way..... Thank you for being a lantern in our lives. You fill our everyday lives with positivity.... You are at your best...

[@DrRehanZafar]

Thank you.

[@MUSLIM_TEAM_MEMBER]

Very nice explaination for medical and other students even every body.

[@maheeraamjad]

Thank you so much sir for such an elaborative briefing this is so helpful :) Keep it up because your videos are helping us to get a clear view at different bioinformatics techniques.

[@sakidezin9806]

It is really a good video. Keep it up.

[@imransattar3036]

my supervisor is so cool that i have to watch videos to continue my work. this one made my day. my first ever comment on utube stay blessed Sir.

[@DrRehanZafar]

Great.

[@imransattar3036]

@@DrRehanZafar sir im having issue to find out crystal structure of crumbs homolog 2 precursor protein. gene is CRB2. for using pymol how and where i can find this structe. didnt find on PDB . kindly help me to get PDB 4 letter code of this protein.

[@DrRehanZafar]

Sure I will let you know.

[@imransattar3036]

Thank you sir.. I'll be waiting for your kind response

[@DrRehanZafar]

Dear PacificWorld TV, there is no PDB matching your need. I have built a model, but it is also of no greater use. For your information, the modeling report is given below as link. I think you should select some domain which then could be modeled using threading based approaches like that provided by itasser. Moreover, you can also move toward ab-initio approaches, but as the protein length is greater so domain specific study will be helpful in reducing the overall time to achieve a good quality model out of this. I recommend that you may discuss this with your supervisor for greater insights into further steps. Best of luck. swissmodel.expasy.org/interactive/5h9f4f/models/report.html

[@InfiniteUniverse88]

It would be nice if PyMol is enhanced by Alphafold 2. Seeing how the protein structure changes as a result of a mutation would be one of the greatest ever boons to science.

[@DrRehanZafar]

You are right and waiting for this feature too.

[@umm-e-habiba3661]

It's truly helpful actually. Thank you so much sir 😊

[@DrRehanZafar]

You are welcome.

[@vickyya3118]

Thank You! An amazing video with clear explanations

[@DrRehanZafar]

I'm happy, that you enjoyed.

[@huzaifa.arshad]

Very Informative. Can you please make a video about "How to use AxPyMOL in PowerPoint"?

[@DrRehanZafar]

Sure the next will be it.

[@huzaifa.arshad]

@@DrRehanZafar Thank you :)

[@zamirhussain3451]

Wonderful dear sir

[@sakidezin9806]

Very nice and soothing.

[@faizaarshad705]

How to delete a protein in megacomplex of proteins? Plz make video on that too

[@gloryparmar2822]

Very helpful video.Sir, can you please make a video about energy minimization of protein structure?

[@DrRehanZafar]

Definitely, I will make the videos related to protein structures after finishing the dashboard part of the current series. Therefore, please stay tuned.

[@xuni_traveldiaries7960]

Nice explanations

[@DrRehanZafar]

Thanks for liking

[@monicagravina7700]

Point mutations should not change drastically the protein structure, but is there any type of structure refinement being performed by pymol after the mutation? (it does not seem like it)

[@DrRehanZafar]

Yes we generally run MD simulations after it. According to our observation, number of mutations is directly proportional to the time of Md step.

[@monicagravina7700]

@@DrRehanZafar If you do not mind sharing, what software/tool/framework do you use for MD? Gromacs? I have been trying to perform mutations with Modeller (mutate model script), but turns out that the optimization is only performed to the side chain of the new residue (that is what I understood after searching explanations about it)... I am new to computational biology field, I used to work with bioprocesses (enzymes), so there are lots of new tools, lots of things to learn... Thank you very much for your insight.

[@DrRehanZafar]

@@monicagravina7700 i will provide you step by step info asap.

[@monicagravina7700]

@@DrRehanZafar Thank you very much.

[@fozshub4915]

Would you please make a video about protein simulation with other proteins in pymol

[@DrRehanZafar]

As far as I can understand the comment. There will be two steps: 1- The interactions of proteins with other proteins will be performed using ZDOCK or HADDOCK software. 2- After they come into close contact then simulations can be performed using AMBER, CHARMM or GROMACS. There is another strategy of simulation known as bownian dynamics simulations. You can also use it. Following paper can be used for this. Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. I will try to make this type of video after some time. At last, I want to say that pymol is only for visualization and some other general purposes but not for simulations.

[@maheswatamoharana4534]

Thank u sir for uploading this vdo

[@DrRehanZafar]

You are welcome.

[@engr.muhammadzafar]

Good

[@ankush_k.s]

How can i randomly mutate a position for all the residue combinations computationally

[@DrRehanZafar]

We have made a small pipeline for that. However, you can use script in UCSF chimera instead of pymol for properly doing it.

[@shirinfth1252]

Thank you that was helpful

[@ceoofthen-word8849]

MASHALLAH

[@Dasha-dc5ny]

Cool, thanks!

[@walia5555]

Sir how mutate amino acid by formylgycine

[@DrRehanZafar]

I will reply you asap.

[@walia5555]

@@DrRehanZafar sir reply

[@jackdelacruz6658]

Hello. Is this pymol software free for students?

[@DrRehanZafar]

Yes, it is free for educational institutes. Please visit this site for the registration. pymol.org/edu/?q=educational/

[@jackdelacruz6658]

@@DrRehanZafar Thank you!

[@muneebajilani1650]

Hi. Can we perform insertions or deletions in a similar manner?

[@DrRehanZafar]

Insertions and deletions can be remodeled using the same protein , however, require simulations afterwards.

[@muneebajilani1650]

@@DrRehanZafar thank you

[@muneebajilani1650]

@@DrRehanZafar I am new at this. Do we use PyMol for simulation afterwards ?

[@DrRehanZafar]

@@muneebajilani1650 we use gromacs, Amber or charmm software for the simulations. Videos regarding Installation and simple simulations by gromacs is in my channel. You can learn from these.

[@aditikonar2411]

In pymol point mutations, is the RMS value same as RMSD?

[@DrRehanZafar]

According to one explanation at research gate: "RMS is the Root Mean Square, whereas RMSD stands for Root Mean Square Deviation.The word "deviation" in the definition of RMSD refers to this: When two structures are compared, a RMS value is measured for each atom and for instance, if you want to compare two structures named Protein 1 and Protein 2: RMSD = Protein 1's atom RMS - Protein 2's atom RMS. RMSD is considered one of the best tools for structural comparison and is calculated by many software, like Pymol and SPDBV." See complete discussion at www.researchgate.net/post/What_is_the_difference_between_RMSD_and_RMS_value

[@aditikonar2411]

@@DrRehanZafar oh its clear now! Thank you 😁

[@DrRehanZafar]

@@aditikonar2411 Welcome

[@faizaarshad705]

please upload the link of use of hydrated residues

[@DrRehanZafar]

Soon I will.