How to create fragments from a ligand?

09 September 2016 0 9K Report

Is anyone aware of any program that can create automatically fragments (chemical probes) from a large ligand that can be used later for fragment based drug design?

Badges
Science topic

More Thomas Evangelidis's questions See All

Which QSAR descriptors are related to ligand entropy?

I am trying to create a ML model which includes various energy terms accounting mainly for the enthalpic contribution to ligand-binding. However, entropic contribution is neglected, although it...

09 October 2019 8,712 5 View

Any good tool for chemical structure extraction from documents?

Could anyone recommend me a good software to extract chemical structures of inhibitors along with the experimental binding affinities from documents (publications)? I don't mind paying for a...

09 October 2019 6,211 1 View

Best protein-ligand sets for docking from DUD-E database?

I am testing a new scoring function for docking and I am looking for simple protein-ligand data sets from DUD-E (only!) in which the binding cavity is well defined and not very flexible. As such,...

07 August 2018 7,730 2 View

Molecular Weight thresholds for training set preparation?

I am training machine learning models to predict the binding affinity of small molecules against a protein receptor. During the training set preparation I remove very small and very big...

06 July 2018 7,927 4 View

Minimum protein-ligand binding affinity difference to claim that a ligand is stronger binder ?

I have a ligand with binding affinity (Kd, Ki, IC50, EC50) measured by a protein-ligand binding in vitro assay. We don't know the experimental error of the measurements. In you experience, how...

05 June 2018 6,879 15 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

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

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

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Z-average size from Dynamic Light scattering can it be lower than the original probe size?

Hi everyone, Recently I have been conducting Dynamic Light scattering experiments in a micellar solution at 5 and gel at 37 degrees of Celsius with latex particles of diameter 190-500 nm. While...

01 August 2024 1,168 4 View

Should I remove an item from a scale to raise Cronbach's alpha and McDonald's omega or is it better to leave it if they are both over .7 already?

Hello! I have this scale which had 10 items initially. I had to remove items 8 and 10 because they correlated negatively with the scale, and then I removed item 9 because Cronbach's alpha and...

01 August 2024 4,606 7 View

Is it true that science is leaving the era of mathematics and entering the era of matrix mechanics?

We assume this to be true. Science leaves the era of mathematics and enters the era of matrix mechanics and the turning point is the discovery of numerical statistical theory called Cairo...

31 July 2024 3,900 2 View