Which proteins of bacteria are often involved in protein-protein interactions with host?

As I know, the effectors and some secretory proteins of pathogenic bacteria are involved in host interactions but I also read some articles where some groups used the whole proteome of bacteria...

11 December 2013 8,609 6 View

Could someone suggest a good pipeline for protein functional annotation?

I have around 20,000 protein sequences of an insect predicted by a gene prediction program.

09 October 2013 7,910 4 View

Is there any resource available from which we can extract the list of genes/proteins involved in social immunity of insects?

I'm interested in the subject of social immunity genes/proteins in insects.

09 October 2013 2,794 4 View

How to remove inparalogs from the orthologous group?

I have a group of orthologous proteins as A A' A" B C D D' E F G H where all alphabets belong to different species; A A' A" and D D' are inparalogs. I want to remove the inparalogs from this group...

08 September 2013 4,415 2 View

What should be the minimum acceptable accuracy of gene-predictor on gene level?

Due to absence of well annotated gene boundaries, I trained a gene predictor in the absence of UTR training parameters. In such condition what can be the minimum acceptable accuracy of...

08 September 2013 6,131 1 View

How to create consensus phylogenetic tree for sequence clusters?

I have several orthologous sequence clusters. I want to create a consensus phylogenetic tree by exploiting these clusters. The number of sequences per cluster varies from 2-13 and the sequence...

07 August 2013 9,509 14 View

Iterative enhancement of ortholog sequence clusters?

I have pHMMs of some ortholog sequence clusters (from orthomcl). I want to add more protein sequences in these clusters. The newly added sequence in these clusters should also fulfill the...

07 August 2013 482 0 View

How to identify and remove inparalogs from the OrthoMcl clusters?

OrthoMCL may group out inparalogs and orthologs together in the one cluster/group. How can we identify such clusters that have "inparalogs"? How can I remove inparalogs. I only want to restrict...

06 July 2013 1,030 1 View

Clustering of protein sequences based on Similarity?

I have 8000 protein sequences that I want to cluster based on similarity (not identity) and select the longest representative sequence from each cluster. I checked several tools like HiFix, SiliX,...

06 July 2013 5,559 4 View

Relating OrthoMCL clusters with Phylogenetics?

I need to relate the OrthoMCL clusters (that I derived from comparison of several insect proteomes) with phylogenetic tree but I am not able to understand how to proceed? I would appreciate your...

06 July 2013 3,456 3 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