about protein modeling

Hello, recently I used I tesser for protein modeling.. But how can I ensure about my modeled protein is perfect or not ? is there any way to make me sure? or any known tools that make me ensure that the model is valid?

Thanks in advance.

snp

• 1,010 views • link

updated 6.5 years ago by Mensur Dlakic

• written 6.5 years ago by fatema19.bge •

I've never tried it myself, but based on a quick google, this looks reasonable? https://www.phenix-online.org/documentation/reference/validation.html

• 0 views • link

written 6.5 years ago by Joe

1 answer

You can validate the stereochemistry of a protein model (see here, here and here) or its energy (see here and here). Neither approach will come even close to guaranteeing that your model is perfect, or even that it is very good.

• 0 views • link

written 6.5 years ago by Mensur Dlakic

Thanks @Mensur Dlakic..

• 0 views • link

written 6.5 years ago by fatema19.bge •

More posts like this

Protein loops
written 2.4 years ago by Curious •

Hello! I'm working with a heteromer protein. In your predicted model a 200aa loop was not well modeled. I tried to improve this part using …
About peptide design
written 5.5 years ago by fatema19.bge •

Hi, I am very beginner in peptide design against a specific protein. I already read some literature about peptide design and I found that they …
energy minimization calculation
written 6.5 years ago by fatema19.bge •

Hi,Recently I modeled a protein using I tesser and then mutate the model using Swiss PDB Viewer.Now I want to minimize the energy by Nomad …
molecular dynamic simulations
written 6.5 years ago by fatema19.bge •

Hello, How can I do my registration in Gromacs? or suggest me the alternate way to use gromacs server? thanks
about snp prediction
written 6.5 years ago by fatema19.bge •

Hi,is there any easiest way to upload rs id's into SIFT input box to find out SNP? It is very tedious and time consuming that …
Validation of protein 3D modelling
written 6.5 years ago by mahafujulislamtonmoy •

Actually I use I-TASSER for protein 3D modelling but I can not valid the model by PDBsum because I can not find out any PDB …
Evaluated Structural consequences of single amino acid mutations
written 9.6 years ago by xcalle91 •

Hi guys, I have a protein around 200 Aa ( which structure is known). I have 3 different sequences of the same protein with one …
ab initio modeling reliability and protein-protein docking
written 11.6 years ago by BI

Hi. I have modeled one protein composed of peptide stretches from different proteins. I have used ab initio modeling to generate my model using phyre2 …
Homology Modeling
written 14.1 years ago by eka0700 •

dear all , I've done homology modeling of a protein using modweb and hhpred .now , how can i do energy minimization or identify the …
Validation Of Homology Model
written 14.1 years ago by eka0700 •

I have done homology modeling of a protein and want to validate it using procheck. but if i do this homology modeling using swiss model …