Please can someone tell me which software should I use to determine the 3D structure of protein without any similar sequence in PDB?

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How to parameterize ligand in MD simulation using VMD-NAMD?

I want to perform MD simulation of protein-ligand complex using VMD-NAMD. When I want to create protein structure file (PSF), there is dialogue box asking me to parameterize my ligand.

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Problem of using command prompt window in molecular dynamic simulation?

I want to perform simulation and when I run the command prompt window with the following syntax " namd2 ubq_ws_eq.conf > ubq_ws_eq.log &" below error will appear" Charm++ fatal error:FATAL...

06 July 2016 1,238 19 View

Problem of accessing VaxiJen - Drug Design Group server?

I have tried several times to access this server (http://www.ddg-pharmfac.net/vaxijen/), but I could not. Can anyone help me with appropriate link to this server

06 July 2016 8,765 2 View

How do I generate DOPE score using multiple template (model_mult.py) in modeller 9.16?

I want to build a model of query sequence (qseq) based on the alignment against the multiple templates using the `model_mult.py'. from modeller import *from modeller.automodel import * env =...

05 June 2016 5,309 4 View

Problem of using NAMD?

I have problem in running NAMD, it usually display fatal error message " No simulation config file specified on command line" despite the fact that I have installed the mpi_x64.msi.

05 June 2016 1,654 0 View

Why do we need molecular dynamic simulation of protein-ligand complex?

Why do we need molecular dynamic simulation of protein-ligand complex? what is the important

04 May 2016 3,662 0 View

How do I refine my 3D model using modeller to minimize energy?

BIOINFORMATICS

04 May 2016 614 4 View

Could you recommend some articles on Urban Transportation System optimization and Innovation?

13 August 2024 2,595 3 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

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How are iso-frequency contours plotted?

Let's say we have a standard, regular hexagonal honeycomb with a 3-arm primitive unit cell (something like the figure attached; the figure is only representative and not drawn to scale). The...

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How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

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How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View