What is the best way to represent the dynamical structure of a protein?

Aravindan Arun Nadaradjane @Aravindan_Arun_Nadaradjane

05 May 2014 1 5K Report

I have a lot of interaction data between two proteins. But, I don't know what is the best way to analyse and represent these data. By interaction data, I know which aminoacid interact to have a contact with the other protein.

Ruxandra-Maria Comisel

Take a look at this option: http://einstein.cs.iastate.edu/PSHOMPPI/index.html

Badges
Science topic

More Aravindan Arun Nadaradjane's questions See All

Creating workflows in Python. I would like to have your opinions about snakemake?

I would like to know the advantages and the disadvantages of snakemake. Is a there a tutorial with multi-threading options? If you have already used snakemake, it would be useful for me if you can...

11 December 2015 1,726 0 View

Is there an alternative for the python module gzip?

I would like to read directly (in python) gzipped files without extraction. Can someone suggest me an other module than gzip? because currently, gzip takes like AGES before It gives me the output...

03 April 2015 4,261 2 View

What is the role of rhodamine 123 in detecting apoptosis?

Thanks in advance.

10 November 2014 2,641 11 View

Can someone recommend research papers or reviews regarding MMP2, MMP3, MMP9, TIMP1&2?

Interaction between MMP & TIMP

04 May 2014 4,695 6 View

Can we find out the different interactions between proteins; especially between amino acids using bioinformatic tools? How?

What is the best way to find out these interactions? Data analysis or observation or the combinaison of these two?

04 May 2014 5,218 6 View

Is there a software to get mutated proteins?

I would like to change an aminoacid in a protein sequence. Can someone suggest me a software? Can I change the sequence directly in the pdb file? If yes, how?

04 May 2014 6,900 8 View

Which is the best software to align sequence?

It can be a DNA sequence, protein sequence.

04 May 2014 7,397 6 View

Can I use the software named AUTODOCK for protein docking?

Please suggest me other softwares if you know.

04 May 2014 465 8 View

What is the use of potential energy distribution (PED) that can be got by the software CHARMM and how can it be exploited?

Use of the software charmm.

04 May 2014 546 3 View

Which is the best software to simulate an interaction between an enzyme and its substrate?

Enzymology

03 April 2014 7,376 10 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Is it possible to use the Fused Deposition Modeling (FDM) to additively manufacture interconnected porous structure generation of >100-200 micrometer?

Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...

09 August 2024 7,892 0 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 2 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

Please explain how the plastic input value should be considered from the true stress-strain curve for the bilinear elastoplastic material model ?

I am working on Abaqus/Explicit(Quasistatic ) for the deformation of the auxetic structure model. Please explain how the plastic input value should be considered from the true stress-strain curve...

05 August 2024 454 3 View