Fatemeh Yaghoobiadeh

11 Questions 37 Answers 0 Followers

Questions related from Fatemeh Yaghoobiadeh

Why pdb file does not upload in iMODS?

Hello everyone. I want to analysis my docked complexes using iMODS server. I successfully analyzed multiple complexes. But for some pdb files I could not upload them and this message appear:...

15 August 2024 6,969 0 View

Population coverage analysis for some MHC II alleles?

Hello everyone Does anyone know how could we determine population coverage of some MHC II alleles such as HLA-DRB3*02:02, HLA-DRB5*0101, HLA-DPA1*02:01-DPB1*05:01, HLA-DRB4*01:01,...

21 June 2024 2,232 1 View

What are non-standard data items in .cif files?

hello every one I open my cif file to edit it. all things apparently are ok, however, enCIFer show some warnings such as "created non-standard data items" for "_symmetry_entry_id cutted" or...

02 April 2024 658 0 View

How could we turn the XRD diffractogram to protein 3D structure ?

Hello everyone I have some problems to analysis the xrd results to get the corresponding 3D structure of my protein with x'pert high score plus. Does enyone have valuable suggestions? Thanks

25 March 2024 4,880 10 View

In silico prediction of immunogenicity of novel mAbs?

Hello everyone Does anyone know a server to in-silico prediction about immunogenicity concerns of a novel mAb? Is C-immsim server suitable to this prediction or it is only suitable to predict...

02 January 2024 5,638 0 View

Troubleshooting of bacterial DNA isolation from Biological samples (especially serum and blood)

hello I want to extract DNA from human serum and blood. unless I tested different extraction methods (such as phenol/chloroform; glass beads; kits; direct PCR on serum samples after some...

01 January 1970 4,657 4 View

Docking problem with autodock 2.4.6

Hello everyone I previously done the protein-protein docking with HEX8.0 software. But for more analysis (e.g. TMSD and s-score) of docking results, I am using the Autodock. I performed all the...

01 January 1970 8,014 2 View

Preparation nitric acid solution with specific weight of 1.2

Hello everyone. I need prepare nitric acid solution with 1.2 specific weight. In our laboratory, we have two nitric acid commercial solutions with 37% and 68.0-70.0% . How could I prepare 1.2...

01 January 1970 5,488 2 View

Analysis the XRD results

Hello everyone 1. Please suggest a robust free software to analysis the XRD results to obtain the corresponding 3d structure of a protein. 2. Is the xrd diffractogram with only a single peak...

01 January 1970 2,097 7 View

Codon Adaptation (using JCat or other tools)

Hello Could anyone introduce a free codon adaptation tool? The URL of Java Codon Adaptation Tool (JCat) does not open for me and I have urgent need to do this and calculate the CAI index and GC...

01 January 1970 9,234 2 View

Error in uploading pdb file for Dynamic simulation by iMODS server

Hello everyone. I want to analysis my docked complexes using iMODS server. I successfully analyzed multiple complexes. But for some pdb files I could not upload them and this message appear:...

01 January 1970 215 0 View