How to make topology file for metalloenzymes (Vanadium dependent chloroperoxidase).I tried by Prodrug server but it fail ?

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Can someone tell me , which vector and strain is best to express Thermomyces lanuginosus lipase in E. coli system?

Actually , i want to express Thermomyces lanuginosus lipase (TLL) in E coli system. so please help me and if somebody have protocol/procedure plz share with me. Thanks in advance!

04 May 2019 9,547 3 View

How can i place a protein in the center of prepared box with different solvents ?

ACtually ,i want to simulate a protein with different types of solvent present like Glycerol+urea+chloride. I created a box with these mix solvents. Now , i am facing the problem is that : how...

31 December 2018 2,682 6 View

How can i calculate number of chloroform molecules in 50% v/v conc. ?

Actually, i want to check effect of chloroform on my enzyme,so i am going for MD simulation with chloroform.But problem is that, i dont know how to calculate number of molecules in 50% v/v conc....

10 November 2017 3,564 5 View

How can i install all packages of Amber 14 (MD simulation) ??

actually ,i want to learn MD simulation on Amber 14 .but i cannot understand ,how to install tLeap etc.and i am confused .so can anybody tell me....easy way to learn that software and please...

08 September 2017 9,465 2 View

How to compile trj_cavity module in gromacs version 5.X on cluster server ??

How to compile trj_cavity module in gromacs version 5.X on cluster server ?? actually ,i want to determine cavities and their volume with respect to time . so, i am trying to install trj_cavity...

03 April 2017 2,911 2 View

Can i use Rosetta Design for mutants design of enzyme ??

actually ,I am working on enzyme design by computational methods ,and i want improve enzyme activity and stability ,so can i used some other tools ?? thanks !!

01 February 2017 4,351 4 View

Which software is most significant for the protein modeling ??

31 December 2015 9,759 0 View

Is there any online server available for virtual screening of inhibitors against an enzyme ??

and how to validation by insilico methods??

01 January 1970 2,398 3 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

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Anyone know how to contact Raymond Streater?

He is emeritus in the mathematics department of King's College London. The email address listed on their web site is not functional. The department has no way of physically contacting him due to...

15 February 2021 5,529 1 View

Can I consider the OOB score of RF model as the same as R^2 score?

In a topology optimization machine learning prediction algorithm, can I consider the OOB score of RF as the same as R^2 score. Could that be a more unbiased way of validating the model

14 February 2021 3,540 1 View

Charmm/GROMACS Residue 'ZN' not found in residue topology database?

I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs. I get an error when doing pdb2gmx Residue 'ZN'...

12 February 2021 9,367 2 View

How to obtain Contig sequence from BAM file?

I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server? I have used Samtools View. That is giving me some sequence but I am not sure whether it...

12 February 2021 3,262 4 View