Why don't we cite Microsoft Excel (generally) in our scientific publications ?

31 December 2015 5,377 5 View

How can I find out sequence similarity between two proteomes ?

10 November 2015 8,686 4 View

How do I tackle frequent data update of NCBI GenBank in Bioinformatics research ?

02 March 2015 4,227 4 View

How can I find out enzymes in large dataset of proteins ?

I have a list of thousands of NCBI-GIs of proteins. I want to determine; 1. how many of them are enzymes ? 2. what are their EC numbers ? 3. What is the reference database for this information...

02 March 2014 6,551 3 View

How to convert gene acronyms to full names ?

I have got a long list of gene acronyms e.g., proS pheS glyQ and so on....... I want to convert them to full names e.g., proS = prolyl-tRNA synthetase pheS = phenylalanyl-tRNA synthetase glyQ =...

01 February 2014 5,869 4 View

Why would two proteins of the same name from the same specie have low similarity?

############################################# UPDATED Now consider following two proteins; http://www.ncbi.nlm.nih.gov/protein/194443845 http://www.ncbi.nlm.nih.gov/protein/194443076 In previous...

01 February 2014 3,491 7 View

Can anybody help me with Geneplotter R package?

Using Geneplotter R package, there is a function named plotMA (http://www.bioconductor.org/packages/2.13/bioc/manuals/geneplotter/man/geneplotter.pdf). To get the plot, your object (data.frame)...

31 December 2013 5,569 1 View

Manipulating DIstance Matrix file created from Clustal Omega (standalone)

I have ~17k amino acid sequences in FASTA format in a single file. Using following command of Clustal Omega on Linux system, I created the distance matrix; clustalo -i filename.faa...

31 December 2013 1,989 4 View

How to determine 'Cluster of Orthologous Groups' for our proteins?

I have a single text file containing amino acid sequence of ~6000 proteins in FASTA format. All proteins belong to a single species, but different strains. I want to determine COG...

31 December 2013 8,600 10 View

What is 'unidentified ORF' ?

There is a protein in Salmonella enterica serovar Typhi with the title "Unidentified ORF" (YP_005216057.1, GI:378958571). What does it mean ? Since as per my thinking, ORF is concerned for nucleic...

31 December 2013 8,717 5 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