How to evaluate the ezyme function using molecular dynamics simulations or other theoretical methods?

I would like to assess few enzyme proteins among the organism to understand the difference in their actions. The structure was modelled using homology modeling and same enzyme having different...

04 May 2019 6,329 8 View

Submission of new ssDNA sequence to database-APTAMER.?

Dear Researchers, We synthesised a novel aptamer against a particular protein/peptide target. Its a ssDNA with 87 bp and we would like to submit it to any database such as NCBI. Can anyone tell me...

10 November 2018 295 1 View

Blood delivery or bbb penetration in vivo procedures?

Can anyone share simple procedure to evalute the brain delivery or blood brain barrier penetration of a molecule. We dont have much facilities so basic or simple procedures are welcome. We would...

08 September 2018 3,395 0 View

How to design an aptamer for peptide/protein in silico?

Hi, How i can design an aptamer for a particular protein/peptide in silico, which help to reduce SELEX time and costs.

03 April 2018 3,276 3 View

Mutations by molecular dynamics simulation?

07 August 2017 3,012 2 View

Docking and missing residues of proteins?

Is it necessary to add missing residues in proteins before performing docking and MD

08 September 2016 4,071 8 View

Molecular dynamics of Modeled protein?

What is the significance of doing MD of modelled proteins. ?

08 September 2016 1,989 3 View

How can i calculate water permeability using Gromacs?

06 July 2016 9,899 6 View

How to Select a PDB file from Protein Data Bank

08 September 2015 8,658 2 View

How to define energy minimization parameters for a cyclic peptide? GROMACS

how and what are the files need to be defined? any manual?

05 June 2015 2,947 7 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 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

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 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