### Binary molecules and the cartridge

cartridge

tutorial

exploration

With a diversion into using PostgreSQL like a document store

### Colliding bits III, expanded

reference

fingerprints

Looking at numbers of collisions and their impact on similarity

### Colliding bits II, revisited

reference

fingerprints

The impact of bit collisions on machine-learning performance

### Timing methods for serializing molecules

reference

optimization

Quickly saving/restoring molecules from text formats

### Dealing with multiconformer SD files

3d

conformers

tutorial

If only we could reliably use better file formats

### Optimizing conformer generation parameters

3d

conformers

optimization

Improving the speed of the RDKit’s conformer generator

### A Ternary GHOST

exploratory

machinelearning

Extending the threshold-shifting algorithm to three-class problems

### R-Group Decomposition and Highlighting

tutorial

prototypes

drawing

rgd

Making pretty pictures for SAR analysis

### Looking at the number of bits set by different fingerprints

fingerprints

reference

How many features do we find?

### Simulating count fingerprints

fingerprints

technical

reference

An approximation to make working with count vectors more efficient

### Fingerprint similarity thresholds for database searches

similarity

reference

FOMO and similarity search

### Thresholds for “random” in fingerprints the RDKit supports

fingerprints

similarity

reference

When is it just noise?

### Looking at random-coordinate embedding

conformers

exploration

3d

An alternative starting point for conformer generation

### Sphere exclusion clustering with the RDKit

similarity

tutorial

Very fast clustering for larger datasets

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