Start with a defined molecule, sequence, structure, or experimental table. OpenScience can help retrieve reference data, inspect structures, calculate properties with available tools, and plan more demanding molecular work.
Choose an input and question
| Input | Example question |
|---|---|
| SMILES or SDF collection | Which records are valid, and how do calculated descriptors compare? |
| Protein structure | Which chains and ligands are present, and what preparation is needed? |
| Protein sequence | What reference record matches it, and which analysis is appropriate? |
| Assay table | Are units, concentrations, batches, and replicate identities consistent? |
| Simulation or spectroscopy output | Which supported parser can extract the required quantities? |
Use Scientific viewers for inspection and Databases for available source collections.
Begin with a small property calculation
Check whether RDKit is ready. Read data/molecules.csv, preserve the input
SMILES and identifiers, and calculate molecular weights for valid rows.
Save invalid rows with the parsing error instead of dropping them. Save
the script and output table in the project.
Check stereochemistry, salts, tautomers, and units before treating two records as equivalent. A computed descriptor is conditional on the molecular representation supplied.
Prepare a structure workflow
Inspect structures/target.pdb. Identify chains, ligands, missing regions,
and preparation questions. Propose a workflow for the stated binding-site
question, including software readiness and required input files. Do not
launch a prediction or docking run yet.
Structure prediction, docking, sequence design, and simulation require different inputs and validation. Use the tool catalog to check the actual support state; reference entries are not automatically runnable integrations.
Use connected scientific tools
The catalog includes connected prediction and design tools where supported. With your NVIDIA API key connected, the NVIDIA BioNeMo NIMs are available through the scientific-capability tool: Boltz-2 and OpenFold2/OpenFold3 for structure prediction, MSA Search for alignments, DiffDock for docking, GenMol and MolMIM for molecule generation, and RFdiffusion with ProteinMPNN for binder design; the protein-binder-design skill chains them the way the BioNeMo Agent Toolkit does. Configure the required personal service access, inspect readiness, and start with a small documented input. Ask for the accepted parameters, expected output files, and cost before a larger task.
Keep predictions, scoring functions, confidence measures, and experimental measurements distinct. A plausible-looking structure or pose is not experimental validation.
Inspect and retain outputs
Save the exact input representation, tool and version when available, parameters, source records, warnings, and output paths. Open generated structures and tables and report failed cases.
For comparisons, use the same preparation and evaluation rules across candidates. Package code, result tables, and a methods note using Saved Results and Team workflows.