Reproducibility and Scientific Interpretation

CADDForge standardizes execution and provenance; it does not establish that a scientific protocol is suitable for a particular target or dataset.

Keep a reproducible record

Preserve input files and checksums, submitted configuration, canonical results, job metadata, logs, pipeline/scatter manifests, component and engine versions, force fields, model identifiers, seeds, platform, and relevant compute settings. Core and bundle versions are different: the bundle pins a tested component set; core implements runtime behavior. Use the version matrix.

Set available random seeds explicitly. A fixed seed does not promise identical results across GPU models, floating-point precision, dependency versions, or parallel schedules. Compare scientific tolerances rather than byte equality for stochastic results. The synthetic introductory examples are deliberately small.

Prepare and interpret molecular inputs

Verify protonation, stereochemistry, bond orders, explicit hydrogens, residue naming, missing atoms, coordinate frame, and force-field compatibility before docking, minimization, MD, or FEP. A successful preparation step is not a guarantee of the intended chemistry. Do not apply experimental interpretations to toy inputs.

Docking scores rank poses within a protocol; they are not measured affinities. Minimization convergence describes an optimization, not equilibration or pose validity. MD and FEP need sampling/convergence assessment and uncertainty appropriate to the method. QM outputs depend on geometry, conformers, electronic structure, solvent model, temperature, and standard state. ML evaluation should avoid leakage between related compounds, fit preprocessing on training data, and report split, metric, and applicability domain.

Units and references

Use explicitly named units such as _angstrom, _ps, and _K where available. Do not infer an energy unit from a generic score or value column. Per-tool reference tables distinguish quantities; inspect the engine's documented units and record conversions. pIC50 is a logarithmic quantity, not a concentration column.

Cite CADDForge's exact component versions and the scientific engines, models, force fields, and methods used. Public method references point to authoritative upstream documentation. A CADDForge citation does not replace the underlying method citations.