Is there any way to find the biological correlation between miRNA and genes?

We are trying to find the biological correlation between miRNA and certain genes. We found the general correlation through IPA (Ingenuity Pathway Analysis). Thank you for your inputs!

05 June 2019 6,900 6 View

Please suggest how should i approach for removal of UMI sequence?

I have mi-RNA sequencing data, where my 3 prime adapter is attached with 12 Nucleotide UMI Sequence (in random manner) along with Reverse Transcriptase primer and Universal Adapter Overall...

31 December 2018 561 5 View

How to merge trajectories after extending simulations in desmond?

I found an explanation in Schrodinger's knowledge base but i am not sure how to run the python scripts in Ubuntu. If possible kindly suggest an easy way. Huge Thanks

08 September 2018 7,715 3 View

Transcription factor binding and expression?

I have a transcription factor protein X and X has a co-activator protein Y. XY bind to the DNA and downstream expression of proteins occur. Now I block the activity of X through inhibitor but dont...

07 August 2018 6,370 7 View

Help with Desmond simulation graph?

Kindly help me interpreting the graph. I am not sure if the ligand is still intact with protein or it has diffused away.

06 July 2018 1,949 6 View

How to carry out membrane protein and peptide simulations?

I want to study the dynamics of ABC transporters along with a peptide molecule which in physiological conditions passes through the transporter. I am clueless how to set the peptide molecule in to...

05 June 2018 6,043 5 View

Help with GROMACS .mdp file parameters?

Hello awesome people, I am new to GROMACS and i have been practicing with different tutorials available online. I successfully ran 1ns simulations. I ran couple of simulations with mdp files as...

01 February 2018 3,515 4 View

Are these normal in Gromacs?

I have following doubts in Gromacs ,and want to know if these things are normal? or i am doing something wrong? 1) The protein is outside the solv box ( picture 1). 2) while i am running...

01 February 2018 7,721 5 View

Software that can find active site itself and dock the protein?

I want to perform protein-protein docking .Please suggest me some software's which can find active site by itself and dock the protein. I have tried HADDOCK but u need to provide active sites in...

08 September 2017 4,589 3 View

Problem with PDB file?

08 September 2017 9,899 8 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 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

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

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View