What is best tool for boolean modelling with limited experimental data?

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

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Efficiency of Proximity Feed Patch Antenna ?

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Please help in identification of this insect?

This insect is minute in size around 1 mm and not clearly visible with naked eye.

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What is causing the raw fluorescence to be negative?

Hi everyone, I would really appreciate it if someone can tell me when and why a raw fluorescence starts below zero. In the picture attached below the blue colour curve starts from a negative...

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How to match the XRD of a compound for which there is no JCPDS file ? Is there any other characterization to claim the synthesis of desired compound?

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Can anyone suggest me broad host range fluorescence expression vectors for Gram-positive bacteria ?

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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

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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?

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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.

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fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

Kushal Suryamohan

You can try using this tool - GeNE Tool (from Eric Davidson's lab) - see attached files. Still in beta testing mode, I think, but it works fine (does tend to hang up abruptly, so my advice - save frequently).

Lori Clow

Curious as to why you want to use Boolean modelling? Typically for describing only two states. Of course, I do not know what exactly you are attempting to achieve. Have you looked at REVEAL (Liang et al.)? Good luck!

Ashmit Singh

@Lori - The objective here is to simulate the pathway with some unreported ligands to define their role in infection. I will also have a look on Reveal.