| Alignment RCSB.org | Calculates overlay of idea vs pre-docked ligand. Displays results in binding site. | JChem Web Services, Structural Calculations | 8 | 4 | Yes | HTTP | internal + external | SSL | JSON | No | JSON | 3D | No |
| Alignment (local/ftp) | Same as above, but protein is fetched from an internal server, not rcsb.org. | JChem Web Services, Structural Calculations | 8 | 4 | Yes | HTTP | internal + external | SSL | JSON | No | JSON | 3D | No |
| Alignment (Lambda + S3) | Same as above, but protein is fetched from S3 folder, and the calculation is run using a Lambda function. | Structural Calculations | 8 | 4 | Yes | HTTP | internal + external | token | JSON | No | JSON | 3D | No |
| Alignment RCSB.org (RDKit) | Same as above, but overlay is calculated with RDKit. | RDKit | 8 | 4 | Yes | Command Line | internal | none | JSON | Yes - SMILES | JSON | 3D | No |
| Calculated Properties | Runs basic med-chem property predictors. | JChem Web Services, all calculators | 4 | 4 | N - can be added | HTTP | internal + external | SSL | JSON | No | JSON | list of numbers | Yes |
| ChEMBL | Returns molecules and activity values from chembl (sim search, high p_chembl value). | JChem Web Services | 1 | | N - can be added | HTTP | external | none | JSON | Yes - SMILES | JSON | molecules, images, numbers | Yes |
| MyChEMBL | Same as above, but using the MyChEMBL local VM. | JChem Web Services | 1 | | N - can be added | HTTP | internal | none | JSON | Yes - SMILES | JSON | molecules, images, numbers | Yes |
| Conformers | Generates lowest energy conformer of a molecule with ChemAxon 3D Alignment | JChem Web Services, Structural Calculations | 4 | | N - can be added | HTTP | internal | SSL | JSON | No | JSON | 3D | Yes |
| Conformers | Generates lowest energy conformer of a molecule with RDKit algorithm. | RDKit | 4 | | N - can be added | Command Line | internal | none | JSON | Yes - SMILES | JSON | 3D | Yes |
| PubChem | Returns substructure matches through PubChem's PUG interface | | 1 | | N - can be added | HTTP | external | none | URL | Yes - SMILES | JSON | molecules, images, numbers | Yes |
| Compliance Checker | Fetches legislative references for a molecule | Compliance Checker | 4 | 4 | N - can be added | HTTP | internal | SSL | JSON | No | JSON | list of links | Yes |
| CRAIS Checker | Fetches legislative references for a molecule | CRAIS Checker | 4 | 4 | N - can be added | HTTP / SOAP | internal | cookie | XML | No | XML | list of links | Yes |
| Compound Registration | Checks a molecule in the corporate registry and returns its ID | Compound Registration | 4 | 4 | N - can be added | HTTP | internal | token + cookie | JSON | No | JSON | molecules, images, IDs | Yes |
| DrugBank | Checks a molecule in DrugBank and returns the closest match | JChem Base | 1 | | N - can be added | HTTP | external | SSL | JSON | No | JSON | molecules, images, IDs | Yes |
| eMolecules | Runs screening compound and starting material search in eMolecules | | 1 | | Yes | HTTP / SOAP | external | token | XML | Yes - SMILES | XML | molecules, images, IDs | Yes |
| eMolecules (local) | Same as above, but uses local ChemAxon Postgres Cartridge for searching | JChem Postgres Cartridge | 8 | 32 | Yes | SQL | internal | SSL | SQL query | No | SQL resultset | molecules, images, IDs | Yes |
| HERG assistant | Return suggested transformations to reduce hERG liability using MMP knowledge base | JChem Web Services, Structure Checker | 1 | 1 | N - can be added | HTTP | internal | SSL | JSON | No | JSON | list of numbers | Yes |
| SureChEMBL | Runs similarity search across SureChEMBL | Madfast Similarity Search | 4 | 8 | Yes | HTTP | internal | SSL | JSON | No | JSON | molecules, images, IDs | Yes |
| Enamine REAL | Runs similarity search across the Enamine REAL database | Madfast Similarity Search | 16 | 128 | Yes | HTTP | internal | SSL | JSON | No | JSON | molecules, images, IDs | Yes |
| Enamine Store | Run searches in the Enamine Store SCR and BB catalog | | | | Yes | HTTP | internal | SSL | URL | Yes - SMILES | JSON | molecules, IDs | Yes |
| MolPort | Runs screening compound and starting material search in Molport | | 1 | | Yes | HTTP | internal | token | JSON | Yes - SMILES | JSON | molecules, images, IDs | Yes |
| Atom economny | Calculates the atom economy of the reaction | | | | N - can be added | HTTP | internal | SSL | JSON | No | JSON | list of numbers | No |
| Carbon Efficiency | Calculates the carbon efficiency of the reaction | | | | N - can be added | HTTP | internal | SSL | JSON | No | JSON | list of numbers | No |
| Patented Reactions | Searches in a patent database of reactions and returns the best match | JChem Base | | | N - can be added | HTTP | internal | SSL | JSON | No | JSON | reactions, images, IDs | No |
| UniChem | Runs duplicate search in UniChem and returns database IDs | | 1 | | N - can be added | HTTP | external | SSL | URL | Yes - InChi Key | JSON | list of links | Yes |
| Reaxys | Runs search in Reaxys and returns compound information and citations | | 1 | | N - can be added | HTTP / XML | external | IP + cookie | XML | Yes - Molfile | XML | molecules, images, IDs | Yes |
| ligprep | Checks the structure with typical rules used by compchems | Pipeline Pilot Components, all calculators | 4 | | N - can be added | HTTP | internal | SSL | JSON | No | JSON | molecules, text | Yes |
| sweet spot analysis | Displays a gradient colored scatter plot of mass and logd values | JChem Web Services, Structural Calculations, Partitioning, Protonation | 4 | 4 | N - can be added | HTTP | internal | none | JSON | No | JSON | scatter plot | Yes |
| CNS MPO | Calculates and displays a radar plot of Pfizer CNS MPO scoring | JChem Web Services, all calculators | 4 | 4 | N - can be added | HTTP | internal | none | JSON | No | JSON | list of numbers, radar chart | Yes |
| logD chart | Calculates the displays a pH-logD chart | JChem Web Services, Structural Calculations, Partitioning | 2 | 2 | N - can be added | HTTP | internal | none | JSON | No | JSON | list of numbers, line chart | Yes |
| Zinc natural derivates | Returns substructure matches from select Zinc subsets | JChem Postgres Cartridge | 4 | 4 | Yes | SQL | internal | SSL | SQL query | No | SQL resultset | molecules, images, IDs | Yes |
| Virtual registry search | Searches the registered ideas in the idea collection while in a design session | Compound Registration | 2 | 4 | Yes | HTTP | internal | token + cookie | JSON | No | JSON | molecules, images, IDs | No |
| MCule | Runs exact match searches in the MCule online catalog | JChem Web Services | | | N - can be added | HTTP | external | SSL | URL | Yes - SMILES | JSON | molecules, IDs, text | No |
| Structure Checker | Checks drawing quality of molecules and offers fixing them | JChem Web Services, Structure Checker | 1 | 2 | Yes | HTTP | internal | SSL | JSON | No | JSON | molecules, text | Yes |
| Structural Alerts | Checks substructure patterns in a molecule like REOS, PAINS, toxiphores | JChem Web Services, Structure Checker | 1 | 0 | Yes | HTTP | internal | SSL | JSON | No | JSON | text, images | Yes |
| ChemLocator | Finds relevant documents based on matching chemical structures in a ChemLocator index | ChemLocator | 2 | 8 | Yes | HTTP | internal | SSL | JSON | No | JSON | molexules, images, text | Yes |
| Toxpredict | Runs toxtree predictions using toxpredict.net | | | | N - can be added | HTTP | external | SSL | JSON | Yes - SMILES | JSON | IDs, text | No |