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

How to calculate Surface electrostatic potential using pymol?

Hi all, please can any guide me on easy way to calculate Surface electrostatic potential of a protein using pymol? or there is any free online server?

31 December 2015 3,022 2 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

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 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

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

What is the production process of CaFe ferroalloys?

I looking for ferro calcium production process

03 March 2021 1,755 4 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...

02 March 2021 4,362 1 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View