The best de novo motif/domain search tool/workflow?

Hello, what is currently the best de novo motif/domain search tool or workflow, if we start from user provided set of protein sequences in FASTA? I have used MEME suite (MEME, DREME, GLAM2) for...

06 July 2018 1,714 5 View

What do you think about doublet genetic code hypothesis?

Recently I have read interesting paper " The triplet genetic code had a doublet predecessor". Patel A. The triplet genetic code had a doublet predecessor.... What do you think about this...

05 June 2018 8,476 6 View

Hello, does anyone know amino acid sequence of BG4 anti G-quadruplex antibody?

I am not able to find it on the internet, nor in supporting information from manufacturer. It would greatly help me in my research... Thanks

04 May 2018 5,877 4 View

Is there any easy way to obtain set of protein FASTA sequences of selected molecular function, pathway, etc.?

Hello, I am interested in obtaining set of all human proteins with the DNA binding ability in FASTA format in one step. Downloading one by one is very tedious for me :-D Do you know any easy...

04 May 2018 4,457 5 View

Is there any user friendly program (online or downloadable) to run BLAST (or something similar) against the custom (local) database?

Hello, I would like to ask if somebody know user friendly way to blast query sequence (protein or nucleotide) against custom (user-defined) database of sequences. Ideally to work on Windows...

04 May 2018 5,172 4 View

Random sampling of FASTA sequences online?

Hello, how to randomly sample set of protein sequences from large file (for example I have defined set of 20 000 protein sequences and would like to sample 200 sequences). Any user-friendly...

04 May 2018 2,053 9 View

Is there any user-friendly tool like ProtParam which enables multiple queries (multiple gene symbols/other identifiers or fasta sequences)?

Hello, please, is there any user-friendly tool like ProtParam which enables multiple queries (multiple gene symbols/other identifiers or fasta sequences)? ProtParam is super tool, but...

04 May 2018 7,092 7 View

What is currently the best user-friendly tool for designing UNIVERSAL PRIMERS?

Hello, I would like to ask what is in your opinion best user friendly tool for designing of universal primers - primers which will amplify target gene of unknown nucleotide sequence (but its...

04 May 2018 7,884 3 View

Does multiple BLAST (or something other) "each to each" exist?

Hello, I am wondering if could be possible to align set of protein sequences (for example 100 protein sequences) each to each by any user friendly way. I.e. sequence no. 1 with the sequence no....

04 May 2018 8,881 11 View

Any experiences with the non-invasive material sampling and methods for intact total RNA isolation from zoo animals?

Hello all, I am wondering if there is any simple way to isolate intact (medium or high quality) total RNA from selected zoo animals. What is the best material for this? Fresh saliva, droppings,...

03 April 2018 9,929 2 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