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Questions tagged [drug-design]

For questions related to the use of materials model in drug design. Examples include simulations of docking, ligand binding, and molecular dynamics of biological species.

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6 votes
0 answers
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Updated book/chapter or review article with broad perspective on computational chemistry

I really like Frank Jensen's "Introduction to Computational Chemistry" because it provides a broad perspective, starting from first principles and extending to surveys of current methods for ...
sunfishstanford's user avatar
5 votes
1 answer
50 views

Identifying Key Chemical Series, Pharmacophores, and Scaffolds in a Large SDF Dataset

Hello fellow computational chemists! I have encountered a challenge that I'd like to discuss and seek advice on. Suppose I have a substantial dataset in SDF format containing thousands of molecules. ...
Poccia's user avatar
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4 votes
1 answer
162 views

How to find topographic distance of molecule from mol format

I have written this code using RdKit to find topographic distance ...
sriram's user avatar
  • 161
1 vote
1 answer
49 views

What are some useful databases for performance-enhancing compounds?

What are some useful databases for performance-enhancing compounds? I've been interested in cognitive enhancers etc.
mavavilj's user avatar
  • 227
2 votes
0 answers
46 views

Any philosophical insight to the concept of "usefulness" in drug discovery? [closed]

Any philosophical insight to the concept of "usefulness" in drug discovery? I mean, I started to naively view drug design and computational drug design as some sort of holy grail (we can ...
mavavilj's user avatar
  • 227
3 votes
1 answer
53 views

Reference-like introductory resources for molecular modelling in drug discovery?

Reference-like introductory resources for molecular modelling in drug discovery? Particularly I want to cover: Underlying chemical phenomena and methods Mathematical methods that have been ...
mavavilj's user avatar
  • 227
6 votes
1 answer
275 views

How to improve my cross-validation R2_score?

I built a prediction model with fingerprints from 300 molecules and got an R2 of 0.9 However when I go to perform a cross-validation I get a very low R2. How can I improve this result? I'm using ...
vorsamaqoy's user avatar
10 votes
1 answer
579 views

Node features matrix with Networkx

I built a function to generate graphs from smiles strings using networkx, inserting various features on the nodes. This is the code: ...
Gianmarco Luchetti 's user avatar
9 votes
1 answer
3k views

How to compute the synthetic accessibility score in Python?

I come from a mainly computer science background, but have become involved in a project related to artificial intelligence-based drug discovery. I made a model that generates novel molecules, for ...
user avatar
10 votes
1 answer
167 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
Paulie Bao's user avatar
  • 3,953
-8 votes
2 answers
353 views

How are quantum computers being used in drug design? [closed]

A biomaterials question this time. How are quantum computers being used in drug discovery and design?
Peter Morgan's user avatar
  • 1,483
19 votes
1 answer
383 views

How established is density functional theory as a tool in drug design?

Motivated by the ongoing COVID-19 pandemic, I am wondering how established density functional theory (DFT) is as a tool/technique in drug design. Drug molecules come in a wide range of sizes from ...
edwinksl's user avatar
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