User: yoosefyud

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yoosefyud40
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2 months ago
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Posts by yoosefyud

<prev • 56 results • page 1 of 6 • next >
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Comment: C: Problem in 3D modelling of ALSIN protein
... Thanks a lot @jgreener. I tried your website which only accepts the 500 residues in each run. I checked the functional domains of ALSIN protein in the NCBI's Conserved Domain Database (CDD). The result is below [https://www.ncbi.nlm.nih.gov/Structure/sparcle/archview.html?archid=13421284][1] As you ...
written 5 months ago by yoosefyud40
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Comment: C: Problem in 3D modelling of ALSIN protein
... I really appreciate your kind and useful response. It completely changed my thought about the protein modelling. Also i want to add that my main purpose is only a simple illustration of model. because my mutation (IN ALSIN case) has resulted in a stop codon with truncated protein. But in other Misse ...
written 5 months ago by yoosefyud40
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Comment: C: Problem in 3D modelling of ALSIN protein
... Thanks a lot for your complete response. Yes, I exactly meant the problem that you mentioned in my previous question which was about another protein. The SWIISS-MODEL can not give good model because of homology modeling problem. I want to analyze the effect of a mutation on this protein. The I-TASS ...
written 5 months ago by yoosefyud40
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Problem in 3D modelling of ALSIN protein
... Hello I'm trying to build 3D model for ALS2 (ALSIN) protein. The websites like SWISS-MODEL can't give proper model. Also, I can't use I-TASSER because the protein is longer than 1500 amino acids. Which software do you suggest to draw proper 3D model for this protein? ...
alignment protein written 5 months ago by yoosefyud40 • updated 5 months ago by jgreener240
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Comment: C: Problem in 3D modelling using SWISS-MODEL
... Thanks a lot for your kind response and guidances. It helped a lot. I'm trying to learn molecular dynamic simulation for complete analysis of mutations effect. But still i haven't been able to find good training source like a book or a videos. Are you familiar with any good training source for molec ...
written 5 months ago by yoosefyud40
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Comment: C: Problem in 3D modelling using SWISS-MODEL
... Thanks a lot for your response. I have a novel mutation and i'm trying to use this database to analyze the effect of mutation on protein folding. If SWISS-MODEL has such problem in some proteins, what are other 3D modeling databases which can be used for my purpose? ...
written 5 months ago by yoosefyud40
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Problem in 3D modelling using SWISS-MODEL
... Hello I am trying to use SWISS-MODEL to draw 3D model for SDCCAG8 protein. My problem is that resulted templates and models do not cover the entire protein sequence properly and a big part of my protein sequence is not involved in modeling. I have the same problem in modeling with CSF1R protein. Any ...
3d modeling protein written 5 months ago by yoosefyud40 • updated 5 months ago by Mensur Dlakic5.8k
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Comment: C: Problem with gromacs
... Thanks a lot it worked! ...
written 6 months ago by yoosefyud40
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Problem with gromacs
... Hello I am using GROMACS 2019.4 on the last version of ubunto. I am trying to fill my box with water solvent but i get the following error > Program: gmx solvate, version 2019.4 Source file: > src/gromacs/commandline/cmdlineparser.cpp (line 276) Function: void > gmx::Co ...
gromacs linux written 6 months ago by yoosefyud40
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Comment: C: Molecular dynamics simulations
... Thanks a lot for your guidance . Yes, it is my first time to run this analysis for novel mutation . Hope i can learn it completely by myself. also, do you know any other source like you tube videos which can help to learn this software? ...
written 9 months ago by yoosefyud40

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Supporter 17 months ago, voted at least 25 times.

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