Accuracy & Reproducibility Policy

Policy (English)

All calculations on this platform are 100% reproducible and based on peer-reviewed, publicly available scientific standards. No proprietary, unpublished, or machine learning black-box models are used. Results are traceable, verifiable, and citable in academic papers & industrial R&D.

Calculation standards

• Molecular weight: IUPAC atomic weights & UniMod modifications
• Isoelectric point (pI): Bjellqvist et al. (1993)
• Peptide properties: Expasy ProtParam
• Hydrophobicity (GRAVY): Kyte & Doolittle (1982)

Other domains (multi-site)

• Oligo: Tm = 2×(A+T) + 4×(G+C) with salt correction (16.6×log₁₀[Na⁺]); ε260 from mononucleotide sum (single-stranded).
• Small molecule: Formula from SMILES (simplified); logP/TPSA from atom contributions; Lipinski rule of five; rotatable bonds from SMILES heuristic.
• Protein: Same as peptide (IUPAC, Bjellqvist, GRAVY); ε280 = 5690×Trp + 1280×Tyr + 120×Cys (Gill & von Hippel).
• Antibody: Peptide engine for MW/pI/GRAVY; CDR1/2/3 by Kabat positions (VH 26–35, 50–65, 95+; VL 24–34, 50–56, 89–97).
• Cyclic: Peptide engine + cyclization mass loss (head-to-tail −H₂O; disulfide −2H).
• PROTAC/ADC/PDC: Combined MW with connection mass loss (−2×H₂O or −n×H₂O per bond).

Version control

We use strict semantic versioning (vX.Y.Z). Any change to algorithms, dictionaries, or parameters increments the version number. All reports include the exact software version for full audit traceability. Current peptide engine version: v2.1.

Official algorithm sources

Peptide (primary)

• Molecular weight: IUPAC atomic weights + UniMod (modifications)
• Isoelectric point (pI): Bjellqvist et al., 1993
• Hydrophobicity (GRAVY): Kyte & Doolittle, 1982
• Reference: Expasy ProtParam

Other domains

• Protein ε280: Gill & von Hippel, Anal. Biochem. 1989
• Antibody CDR: Kabat et al. numbering
• Oligo Tm: Wallace-style + salt correction; ε260 mononucleotide values

Version numbering

Format: v major.minor.patch. Any change to algorithms or dictionaries requires a version bump; no silent modifications.

• v1.0.0 — Initial release
• v1.0.1 — Bug fix (e.g. minor calculation correction)
• v1.1.0 — New feature or dictionary
• v2.0.0 — Major algorithm change

Reference test cases

Run before each release to verify correctness (npm run test). Reference: IUPAC, Bjellqvist, Expasy ProtParam.

Core principles

• All algorithms = published, authoritative standards; no ad-hoc or unpublished methods.
• All dictionaries = fixed version; no silent updates.
• All calculations = reproducible, traceable, auditable.
• All results = include version + citation; any change = version bump.