Ameya Dipak Bendre

9 Questions 32 Answers 0 Followers

Questions related from Ameya Dipak Bendre

Is there any online server or standalone (GUI for windows) tool to annotate genome (not metagenome)?

I want to annotate all genes from the genome sequencing data of a bacteria (nanopore method). I am not very well versed with Linux nor do I have access to a workstation. Is there any online...

05 July 2022 5,147 0 View

What is the sequence of RBS in pMynt-Kan vector?

I purchased the vector pMynt-Kan from addgene. It is used for mycobacterial heterologous expression. The map does not show RBS in its features. Could anyone please tell me how to identify the RBS...

03 August 2021 927 0 View

How to make library of molecules for screening against target protein structure for structure based drug design?

I have a 3D structure of a target protein. I have two of its inhibitors but are not suitable to develop into lead molecules. I wish to perform virtual screening against it for structure based drug...

03 July 2020 8,811 4 View

How to solublize membrane anchored recombinant protein during purification?

Hi, I am working on a protein which is known to anchor in the membrane post translation. I am recombinantly expressing it in E. coli and on lysis the protein is detected in pellet fraction and not...

05 February 2020 4,356 4 View

How to calculate RMSD of selected region from a crystal structure?

I want to compare about 10 amino acid long loop region of a protein with similar region from other structures. Which software/tool/server could be used for the same to calculate the RMSD of these...

28 March 2018 3,789 3 View

Which is simplest and reliable tool to perform thermal simulations of a protein or protein-protein complex?

I want to study thermal stability and structural transitions occurring in a protein over a range of temperatures say from 20 to 90C. Which tool can be used? Is there any online server? Or which...

31 January 2018 8,496 3 View

What does the minima at 230nm in CD spectra of a protein-protein complex indicate?

I recorded far UV CD spectra for two of my proteins and their complex. Both proteins mainly contain beta sheets connected by loops. The protein (say A)which has no alpha helix gave minima around...

14 September 2017 2,159 3 View

Which is more potent inhibitor when dissociation constant is given in Moles (higher or lower Kd value)?

I have calculated dissociation constant for an enzyme inhibitor (say A) which is about 500nM. The dissociation constant for similar inhibitor from other species (say B) is about 1.5microM. Based...

07 September 2017 1,020 2 View

Any databse/ server to analyse signal peptide?

Using SignalP server I identified a signal eptide in my protein sequence. I want to analyse the signal peptide in detail. Is there any bioinformatic way ( a tool or a server) that is dedicated for...

15 July 2016 6,986 3 View