How can we integrate signaling networks obtained from different databases?

More Shishir K Gupta's questions See All

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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

Scott Lett

BioPathwise can perform computer-assisted merge and compare pathways, but it doesn't work with Biopax 3 format. If you can translate to SBML format, it may work for you. I think you can get free access to BioPathwise at the Mount Sinai School of Medicine PRIME website http://tsb.mssm.edu/primeportal/

Shishir K Gupta

Dear Scott,

Thanks for your reply but unfortunately I could not find the solution of my problem in BioPathwise.

Thanks.

Anvesh Yalamanchali

http://www.ebi.ac.uk/biomodels has almost all the models on signaling networks. Are you looking to do integrate your information and do dynamic analysis or do you just want to create a protein-protein interaction graph?? As to my knowledge one has to do it manually by either changing your code (SBML or Biopax) or use celldesigner and create your own network. But, if you want to do a dynamic analysis of your network behavior then it is a whole different story.