Does anyone have experience with pharmacophore modelling for two same ligands in same binding pocket?

I have a protein (crystal structure) complexed with two molecules of the same ligand (inhibitor). I am trying to build a pharmacophore model for searching potential hits. But the problem is that...

06 July 2013 4,807 14 View

Is it possible to develop a pharmacophore model from DNA-PROTEIN interaction sites?

If yes, what are the software/online tools/servers for doing this?

04 May 2013 1,736 1 View

What are the criteria of choosing descriptors?

I would like to know what should be the criteria in choosing descriptors? For example: In MOE, one can calculate 100's of descriptors. But those all descriptors, obviously, can not be used for...

08 September 2012 4,747 16 View

Regarding the reliability of MOE for bioinformatics

Can anybody please suggest what the status of the MOE software package is? How reliable is it in Pharmacophore modeling, QSAR and docking studies?

06 July 2012 3,307 6 View

PC configurtion

Can anybody suggest me the best PC configuration used to run Molecular dynamics and docking in Schrodinger package?

04 May 2012 2,878 0 View

Protein structure prediction

My aim is to find a better lead compound by in silico approach. The crystal structure of the protein which I am working upon is not yet available, so I performed Blastp against PDB but no good...

04 May 2012 5,176 33 View

Showing secondry structural elements with the aligned amino acid sequence

Can anybody help me in using ESPript (http://espript.ibcp.fr/ESPript/ESPript/). I want to show the secondary structural elements with the aligned sequence. When I upload alignment file in...

04 May 2012 6,371 7 View

Need help regarding NAMD or Desmond

Can anybody help me with the working of NAMD or Desmond for molecular dynamics study of proteins??? Many thanx in advance.

01 February 2012 4,601 6 View

Training and test set in comfa

What is the basis of selecting training and test set in CoMFA???

09 October 2011 3,031 5 View

non-polar interaction visualization

hellow everybody, i have my docking complex (DNA-LIGAND) from Glide but unable to show non-polar interactions in maestro as well as in other softwares like PyMol, SPDBV, Chimera and VMD. please...

06 July 2011 8,471 7 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