Are there any alternative websites for archiving theoretical protein structures?

More Bhaskar Ganguly's questions See All

How to find pathways for a set of proteins?

I have a list of about 800 Uniprot IDs. What would be a good way to know the common pathways in which these proteins participate?

11 December 2018 2,669 3 View

How well does ELISA compare with LC-MS for quantitation of antibiotic residues in food?

Most available literature considers spectrometric methods, mostly LC-MS, as the gold standard for quantitation of antibiotic residues, and ELISA has largely been regarded as a screening test....

04 May 2018 7,169 3 View

Any alternatives for heteroclitic peptide calculations other than MHCPred?

The MHCPred server (http://www.ddg-pharmfac.net/mhcpred/MHCPred/pepLib.html) does not seem yo be functional. Can anyone suggest any alternative free-to-use webserver or freeware for heteroclitic...

07 August 2017 8,440 3 View

What is the best computational method to test the evolutionary relationship between two proteins?

During the analysis of one particular enzyme of my interest (of animal origin), I have stumbled upon another enzyme of plant origin that has similar sequence and motifs. What would be the best...

08 September 2013 4,026 17 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

How to calculate CCS for Sodiated adduct ions and Multiply Charged Ions?

I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...

08 August 2024 8,329 0 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 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

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Is it necessary to covary exogenous constructs in a structural model?

I am working on a SEM model where i have 7 latent variables (6 exogenous and 1 endogenous). In AMOS when I co-vary the exogenous constructs, only 2 paths are coming significant out of 6. But when...

03 August 2024 6,028 4 View

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

In SEM, if a latent variable consists of three observed variables, and each observed variable has four items, what should I do?

Suppose I am studying the construct of "Academic Motivation" (latent variable) in students, which is measured through three observed variables: "Intrinsic Motivation," "Extrinsic Motivation," and...

31 July 2024 3,913 6 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 View

Bhaskar Ganguly

I am delighted to report that the PMDB is now available at a different URL. :D

https://bioinformatics.cineca.it/PMDB/

Carlos A H Fernandes

The reported above link (http://bl209.frm.uniroma1.it/PMDB/) it is unavailable. Does anyone know what the link is working for access the PMDB or any alternative websites for archiving theoretical protein structures?

I have been using ModelArchive (http://www.modelarchive.org) to deposit theoretical protein structures.