Journals for molecular dynamics

More Rajiv Lakkaniga's questions See All

How to desalt zwitterions?

I am trying to synthesize a compound which has both carboxylic acid and amine. During the purification, when I do the pH adjustment it forms a zwitterion and goes into the aqueous layer. Is there...

01 February 2020 6,975 3 View

How do cancer cells grow without tumor microenvironment?

In the body, when one develops a tumor, the microenvironment is very important. How do the cell cultures of cancer cells grow in the flasks without that micro-environment and only with the media...

01 February 2020 3,132 4 View

What are the alternatives for FBS in cell culturing?

I am trying to grow cancer cells and do MTT assay for drug screening. Are there any alternatives to FBS? I know that FBS and FCS are widely used for cell culturing, but I am looking for other...

31 December 2019 4,886 4 View

How does protonation of aminoacids in cellular environment occur?

Some proteins change their conformation based on protonation state of particular residues like aspartic acid. Some kinases are examples for this. For example, in case of Abl kinase, protonated...

10 November 2019 5,493 5 View

Will running very long molecular dynamics cross the energy barriers and explore different conformations?

I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by...

09 October 2019 5,906 3 View

How to analyze the van der waal's interactions of a residue through a simulation?

Is there a way to quantify (eg.: plots) the van der waal's or other hydrophobic interactions of a residue through a simulation? For example, using VMD, we can check for salt-bridges and hydrogen...

07 August 2019 893 3 View

Any TLC stain to detect presence of boron/boronic acid?

I am trying to synthesize boronic acid pinacol ester derivatives from aryl/hetero-aryl halides. Is there any TLC staining technique which can indicate the formation of boronic acid? Thanks.

03 April 2019 685 10 View

Are there any bioisosteres of triple bond?

Are there any bioisosteric replacements of triple bond (alkyne) which were employed for lead optimization or scaffold hopping? Thanks.

03 April 2019 2,895 5 View

Is HATU((1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluorophosphate)) stable upon heating?

I am doing an amide coupling reaction using HATU. The starting material is not very soluble in DMF. So, I am thinking of heating the reaction mixture to 65C. Is HATU stable at that temperature or...

08 September 2018 3,612 3 View

What is a collective variable in metadynamics?

I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.

07 August 2018 5,831 4 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

Can I use a HisTRAP column for affinity chromatography?

I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...

07 August 2024 505 3 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

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

Research Methodology - Impact of Corporate Reputation on Stakeholders Behaviors?

Please can anyone support with the survey questions based on RQ measures and propose how to do it in FMCG industry and include as well the role of brand equity Thanks

06 August 2024 949 0 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

Anyone having idea about VN primer for miRNA primer design ?

How to design VN primer to attach with universal reverse primer

05 August 2024 2,116 3 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

Martin Klvana

https://www.ncbi.nlm.nih.gov/nlmcatalog/journals

Muthusaravanan Sivaramakrishnan

Bioinformation, computational biology and chemistry, bioinformatics, journal of molecular modeling....

Vijayan Ramachandran

RSC advances, PLOS computational biology, BBA, PLOS one etc.,

http://www-jmg.ch.cam.ac.uk/data/c2k/cj/comp.html

Uttam Pal

Submit to the Journal of Proteins and Proteomics (https://www.springer.com/biomed/journal/42485).

Sargol Mazraedoost

Check in these links. It might help you.

https://www.omicsonline.org/scholarly/molecular-dynamics-journals-articles-ppts-list.php

Good Luck.