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”

./aloha.html

Toy continuous problems

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

./toy_continuous_problems.html

White noise

White noise drawn from a unit Gaussian

./white_noise.html

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.

./albuterol_similarity.html

Amlodipine MPO (using tdc)

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

./amlodipine_mpo.html

Celecoxib rediscovery (using tdc)

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

./celecoxib_rediscovery.html

Decorator Hop (using tdc)

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

./deco_hop.html

dockstring for ligand design

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

./dockstring.html

DRD2 docking (using tdc)

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

./albuterol_similarity.html

DRD3 (or 3pbl) docking (using tdc)

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

./drd3_docking.html

Fexofenadine MPO (using tdc)

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

./fexofenadine_mpo.html

GSK3β (using tdc)

The Therapeutics Data Commons’ implementation of the GSK3β oracle.

./gsk3_beta.html

Isomer C7H8N2O2 (using tdc)

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

./isomer_c7h8n2o2.html

Isomer C9H10N2O2PF2Cl (using tdc)

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

./isomer_c9h10n2o2pf2cl.html

JNK3 (using tdc)

The Therapeutics Data Commons’ implementation of the JNK3 oracle.

./jnk3.html

Log-solubility (LogP)

Computing the log-quotient of solubilities using RDKit.

./rdkit_logp.html

Median 1 (using tdc)

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

./median_1.html

Median 2 (using tdc)

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

./median_2.html

Mestranol Similarity (using tdc)

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

./albuterol_similarity.html

Osimetrinib MPO (using tdc)

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

./osimetrinib_mpo.html

Penalized Log-solubility (LogP, using lambo)

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

./penalized_logp_lambo.html

Ranolazine MPO (using tdc)

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

./ranolazine_mpo.html

Scaffold Hop (using tdc)

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

./deco_hop.html

Sitagliptin MPO (using tdc)

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

./sitagliptin_mpo.html

Synthetic Accessibility (SA, using tdc)

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

./sa_tdc.html

Thiothixene rediscovery (using tdc)

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

./thiothixene_rediscovery.html

Troglitazone rediscovery (using tdc)

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

./troglitazone_rediscovery.html

Valsartan SMARTS (using tdc)

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

./valsartan_smarts.html

Quantitative Estimate of Druglikeness (QED)

Computing the QED using RDKit.

./rdkit_qed.html

Zaleplon MPO (using tdc)

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

./zaleplon_mpo.html

Proteins

Protein SASA score (using foldx)

Solvent accessibility of mutations of a wildtype using foldx

./foldx_sasa.html

Protein Stability (using foldx)

Stability of mutations of a wildtype using foldx

./foldx_stability.html

Protein Stability (using PyRosetta)

Stability Predictions of variants from a wildtype.

./using_poli/objective_repository/Rosetta_energy.html

Protein Stability (using RaSP)

Rapid Stability Predictions of single mutations from a wildtype.

./RaSP.html

RFP Fluorescence Protein Stability (using lambo)

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

./foldx_rfp_lambo.html

Other

Mario jumps

Optimizing the number of jumps on a Super Mario Bros level

./super_mario_bros.html