WHy the docked substrate move out from the active site of the protein during MD simulation?

I have docked the substrate in the active site of the protein ( contains NAD and lactate substrate ), interacting with binding residues through hydrogen bonding. When i start the MD simulation...

31 December 2018 6,931 11 View

How to correct the number of coordinates in gromacs file (solv.gro, topol.top)

Respected All, I am going to do the Ligand MD simulation using Justin Lemkul tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/03_solvate.html). After...

31 December 2016 156 4 View

Which statistical test is appropriate for unequal sample size with less mean difference?

I have worked on vocal behavior of rats during a diseased condition and found 8 different type of calls but of unequal size with less difference among means in their temporal parameters despite...

05 June 2016 8,770 3 View

What is the relatioship between the potentail energy and protein structure?

I have modeled a wild protein structure and their five mutant structure. Now i have analyzed their potential energy for normal and mutants. Potential energy calculated for wild, Pro420Arg,...

31 December 2015 8,947 10 View

Can anyone explain why I have a failure while running an MD simulation using MOE software?

09 October 2014 9,671 2 View

How to find the sequences responsible for the aerobic nature of the enzyme through phylogenitic analysis?

Hello, I have amino acid sequences of the same enzyme in more than 150 different organism which is grouped in two form i.e Aerobic and anaerobic enzyme. I did blasting of these sequences but i...

01 January 1970 266 1 View

How to merge two subunit of protein through linker by homolgy modeling?

Hello, I have two subunits (let say alpha and beta) between them a linker sequence (29 amino acid). I have modeled the alpha and beta subunit using templates extracted from PDB. There is no...

01 January 1970 2,872 12 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Can we distinguish the type of free fluid inside the pelvic and abdominal cavities whether blood or serous fluid using the ultrasound?

during ultrasound examination of acute abdomen, sometimes we see free fluid , can we know the type of fluid ,whether blood or not , using ultrasound only? if yes , what are the sonographic...

01 March 2021 7,476 4 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Can Virtual Servers (remote dekstop manager) run heavy ANSYS Fluent CFD simulation ?

I have a virtual machine. My host Pc specs are not that good thats why i went for virtual servers. so basically my host pc has 8gb of ram with nvidia quadro k2200 4Gb DDR5 GPU ,processor intel...

01 March 2021 8,415 1 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

Is there an open source free software for text mining and sentiment analysis?

I am looking for a free software for text mining and sentiment analysis for my research on customer review mining (it involves calculating polarity of attributes,opinion oriented information...

25 February 2021 1,920 6 View

Which are the journals for free paper publication?

A bunch of flower for everybody. I would like to ask about the list of journals which we can publish our paper for free. Thanks in advance. Sincerely Walid

25 February 2021 9,790 3 View

Suggestions for occupational stress surveys?

I am currently writing a masters thesis on reasons for occupational stress in the early childhood classroom, and want to include a short survey assessing participants work-related stress levels. I...

24 February 2021 8,678 2 View