Yi-Ching Tang

New DrugComb data

4

**Describe the problem** The DrugComb database has released new drug combination and monotherapy screening datasets, which includes cancer, malaria, and COVID-19. Reference: [[https://doi.org/10.1093/nar/gkab438]](https://doi.org/10.1093/nar/gkab438) **Describe the solution you'd like** Replace current...

Request to add required packages

1

Hi, There are some missing references for the provided scripts. Is it possible to list at least the following packages required for classification_TU.sh, classification_OGB.sh, and classification_ZINC.sh? Thanks. ```{python} $ sh...

Unit in the openmm_relax function

1

Hi, It seems that the openmm's Simulation.minimizeEnergy() method has a default unit set to **kilojoule/model**, while **kilocalories_per_mole** was used at the beginning of the openmm_relax function in the script [relax....

Does optimize_ab.py support multiple CDRs?

3

Hello, Could you suggest a way to optimize multiple CDRs? I've tried two options, but I need help to get them to work. 1. --design_contig "95-102" 2. (all) ``` File...

Interpretation of predicted mutation effect

1

Hello, Can you tell me how to interpret the score appropriately? Does it have a unit, like ΔΔG in kcal/mol? Is the score comparable? What is the difference between effects...

InSty: NameError: name 'Interactions' is not defined

9

Which module is this Interactions class dependent on? `interactions = Interactions()` http://www.bahargroup.org/prody/tutorials/insty_tutorial/insty_tutorial.pdf

Hello, Could you advise me on resolving this error? > **ERROR: No matching distribution found for pytorch_lightning==1.6.3** I followed the instructions and tried several workarounds but still had no luck....