Any software for determining torsional angles from protein crystal structure???

More Sujeesh Sukumaran's questions See All

Does IDPs have higher sensitivity in NMR compared to structured proteins?

Due to high flexibility IDPs expected to have higher sensitivity in NMR compared to structured proteins. Is this hypothesis correct? If yes can you suggest a suitable reference for this?

04 May 2019 8,775 2 View

Which buffer to use for NMR study peptide - Zinc interaction?

I am studying interaction of zinc with a peptide. Which buffer should I use ? And what is the highest concentration of zinc can used ?

08 September 2018 1,440 3 View

What is the protocol for monitoring Abeta (1-40) aggregation by ThT fluorescence assay ?

I want to study aggregation kinetics of Abeta (1-40) by ThT. I would like to know the working protocol for this study. I am using plate-reader based assay.

08 September 2018 5,167 0 View

How to compare stability of a protein and its mutant with NMR spectroscopy?

How can we compare stability of two proteins with the help of NMR spectroscopy? what are the traditional NMR techniques that we use for this purpose?

11 December 2017 3,766 4 View

What are the properties to be considered while designing a peptide for preventing Amyloid beta aggregation ?

If I design a peptide for preventing aggregation of Abeta 42 peptide, what are aspects should I consider if I want to suggest it as drug for Alzheimer disease. What all are the properties should...

10 November 2017 3,234 2 View

How to check presence of calcium in a protein sample?

I have a calcium binding protein. To make it calcium free i did dialysis with EDTA containing buffer. But how to make sure whether a protein is calcium free ?

10 November 2016 5,580 2 View

Can any one suggest some good reviews on Calcium binding proteins (especially crystallins) ?

In search of some review article on calcium binding proteins and exploring studies that can be performed on them.

05 June 2016 7,727 1 View

What are the disadvantages of CellSeearch System for capturing CTC ?

I read about circulating tumor cells and understood that cellsearch (Janssen) is the only FDA approved method that existing for capturing cancer cells and they are based on antigen-anibody...

10 November 2015 4,624 7 View

Why is DH5alpha better than BL21 for plasmid isolation?

Why do we generally prefer cells like DH5alpha or top10 for increasing plasmid amount and isolation? Why are we using BL21 for protein expression? Why not DH5alpha?

10 November 2014 3,629 10 View

How to express a protein with N-terminal cysteine?

I have a protein of 277 aminoacids. I want express a truncated version of that without first 22 aminoacids from N-terminal and also the sequence should start with a cysteine residue. Is there any...

04 May 2014 3,791 10 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

How to solve g_mmpbsa error?

Program: g_mmpbsa, version 2024.1 Source file: extrn_apbs.cxx (line 152) Fatal error: Failed to execute command: $APBS pybYcUWA.in --output-file=pybYcUW.out

07 August 2024 6,066 0 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

How to understand this crystallographic phenomenon of low temperature crystals in zeolite?

During low-temperature testing, new diffraction peaks that appear could be indicative of several phenomena. In one of our tests, we observed notable new peaks around 40° and 45° in a specific...

06 August 2024 726 3 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

Why Powder XRD is performed after cruhsing a crystal if Single Crystal XRD analysis of the same crystal has been performed already ?

What information we can get from PXRD analysis other than from SCXRD analysis of a crystal ?

30 July 2024 6,261 4 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

How to know the b axis of a single crystal?

How to apply magnetic field parallel to b axis of any crystal

29 July 2024 4,083 2 View

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 View

Sk Jahiruddin

Torsional angle can be measured in any visualizer like VMD, PyMoL, Chimera etc. VMD is easy. It has very good tutorial also.

Francisco J. Enguita

I agree with the suggestions about Pymol, Chimera... Just to add another software, try Coot. You have a Windoze version if you like.

http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot.html

Good luck. Best

Paco

Sujeesh Sukumaran

Thank you..