Is the any software for finding upstream and downstream sequence of a gene?

For cloning purpose when we design primers, we need to deal with the upstream and downstream sequence of the cDNA. could you please suggest a software which would be appropriate in doing that?

06 July 2016 9,275 7 View

How to incorporate amino acids in the excel sheet ?

Hi Everyone, We want to develop a sequence database of protein. In the excel, we want to incorporate one letter code of amino acids in individual cells of the database. This would be extremely...

04 May 2016 860 2 View

How we could calculate the range of phi and psi angle between a monopeptide.

For example, attached file is representing a .pdb file containing a peptide between two glycine. How we could measure the range of phi and psi angles here. Thanks in advance for your help and...

01 February 2016 3,067 4 View

Which one of the following would be a suitable method to calculate the binding affinity/binding free energy of a protein ligand interaction?

02 March 2015 5,875 1 View

How to model a protein with multiple domains and no template covering more than one domain?

I'm trying to model a protein which has multiple domains and templates available covering small parts of the sequence. It is a 4500 aa protein and to moderately covering the sequence it needs 7...

11 December 2013 2,860 19 View

Double Conformation of amino acid residues in a PDB file while runing MD Simulation

I'm preparing a PDB to run a MD simulation in AMBER. I have noticed that some of the amino acid residues exist in double confirmation. Should I remove all the double confirmation before the...

06 July 2013 1,819 3 View

Can someone recommend a good theoretical method by which two mutant variants could be differentiated?

Stability of protein mutants: I'm trying to design thermostable variants of a protein. Is it possible to theoretically differentiate them without doing simulation? What would be the parameters I...

06 July 2013 4,758 5 View

How to relate loop flexibility with enzyme catalysis?

I'm working with an enzyme where some of the loops are playing important roles in catalysis. How could I study the relation of loop flexibility with the re-activity (computationally)?

05 June 2013 3,213 6 View

Can anyone help me with a suitable method for computational study of the thermal stability of protein mutants?

I'm studying stability of certain enzymes with their mesophilic and thermophilic homologues using MD Simulation methods. Using the information obtained from the study I'm trying to design point...

05 June 2013 2,959 3 View

I need help with my MMPBSA calculation

I am running a binding energy calculation (MM-PBSA) for protein-ligand complex using Amber11 and AmberTools 1.5. I am following a Ross Walker tutorial (Link:...

01 February 2013 3,412 0 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