All objective functions

These are all the objective functions available on poli. Click on one of them to get a minimal working example of how to use it.

Toy problems

Aloha

A toy example about optimizing 5-letter words to spell “ALOHA”

Toy continuous problems

The usual benchmark functions for continuous optimization (e.g. easom, or ackley_function_01)

White noise

White noise drawn from a unit Gaussian

Small molecules

Most of our problems are based on the PMO benchmark, by Gao et al [Gao et al., 2022], which extends the GuacaMol Benchmark proposed by Brown et al [Brown et al., 2019].

Albuterol Similarity (using tdc)

The Therapeutics Data Commons’ implementation of the Albuterol similarity oracle of GuacaMol.

Amlodipine MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Amlodipine MPO oracle of GuacaMol.

Celecoxib rediscovery (using tdc)

The Therapeutics Data Commons’ implementation of the Celecoxib rediscovery oracle of GuacaMol.

Decorator Hop (using tdc)

The Therapeutics Data Commons’ implementation of the “deco Hop” oracle of GuacaMol.

dockstring for ligand design

Using dockstring to assess the docking score of a small molecule.

DRD2 docking (using tdc)

The Therapeutics Data Commons’ implementation of the DRD2 docking oracle.

DRD3 (or 3pbl) docking (using tdc)

A wrapper around the Therapeutics Data Commons implementation of 3pbl docking.

Fexofenadine MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Fexofenadine MPO oracle of GuacaMol.

GSK3β (using tdc)

The Therapeutics Data Commons’ implementation of the GSK3β oracle.

Isomer C7H8N2O2 (using tdc)

The Therapeutics Data Commons’ implementation of the first isomer oracle of GuacaMol.

Isomer C9H10N2O2PF2Cl (using tdc)

The Therapeutics Data Commons’ implementation of the second isomer oracle of GuacaMol.

JNK3 (using tdc)

The Therapeutics Data Commons’ implementation of the JNK3 oracle.

Log-solubility (LogP)

Computing the log-quotient of solubilities using RDKit.

Median 1 (using tdc)

The Therapeutics Data Commons’ implementation of the “median 1” oracle of GuacaMol.

Median 2 (using tdc)

The Therapeutics Data Commons’ implementation of the “median 2” oracle of GuacaMol.

Mestranol Similarity (using tdc)

The Therapeutics Data Commons’ implementation of the Mestranol similarity oracle of GuacaMol.

Osimetrinib MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Osimetrinib MPO oracle of GuacaMol.

Penalized Log-solubility (LogP, using lambo)

Computing the penalized log-quotient of solubilities using lambo’s implementation.

Ranolazine MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Ranolazine MPO oracle of GuacaMol.

Scaffold Hop (using tdc)

The Therapeutics Data Commons’ implementation of the scaffold Hop oracle of GuacaMol.

Sitagliptin MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Sitagliptin MPO oracle of GuacaMol.

Synthetic Accessibility (SA, using tdc)

A wrapper around the Therapeutics Data Commons implementation of the synthetic accessibility oracle.

Thiothixene rediscovery (using tdc)

The Therapeutics Data Commons’ implementation of the Thiothixene rediscovery oracle of GuacaMol.

Troglitazone rediscovery (using tdc)

The Therapeutics Data Commons’ implementation of the Troglitazone rediscovery oracle of GuacaMol.

Valsartan SMARTS (using tdc)

The Therapeutics Data Commons’ implementation of the Valsartan SMARTS oracle of GuacaMol.

Quantitative Estimate of Druglikeness (QED)

Computing the QED using RDKit.

Zaleplon MPO (using tdc)

The Therapeutics Data Commons’ implementation of the Zaleplon MPO oracle of GuacaMol.

Proteins

Protein SASA score (using foldx)

Solvent accessibility of mutations of a wildtype using foldx

Protein Stability (using foldx)

Stability of mutations of a wildtype using foldx

Protein Stability (using PyRosetta)

Stability Predictions of variants from a wildtype.

Protein Stability (using RaSP)

Rapid Stability Predictions of single mutations from a wildtype.

RFP Fluorescence Protein Stability (using lambo)

LaMBO Fluorescence (RFP) by stability and solvent-accessible surface area.

Other

Mario jumps

Optimizing the number of jumps on a Super Mario Bros level