Thomas Evangelidis

6 Questions 11 Answers 0 Followers

Questions related from Thomas Evangelidis

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...

10 October 2019 6,070 1 View

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...

10 October 2019 8,631 5 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,...

08 August 2018 7,666 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...

07 July 2018 7,872 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...

06 June 2018 6,814 15 View

How to create fragments from a ligand?

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?

09 September 2016 8,653 0 View