Long-form explanations written for students, researchers and anyone who works with peptides. Each guide starts from first principles, uses worked examples calculated with the tools on this site, and lists the primary literature it draws on.
What each tool on this site computes, where the numbers come from, and how to avoid the most common mistakes when using them.
How peptide mass is built from residue masses, and how disulfides, amides and counterions change it.
Read βHendersonβHasselbalch step by step, why calculators disagree, and pI in the lab.
Read βWindow size, the transmembrane threshold, GRAVY, and where hydropathy plots mislead.
Read βThe chemistry and biology every peptide shares: the bond itself, the bridges and modifications that shape peptides, how they fold, and what they do.
Why the amide bond is planar, what cis and trans mean, and how the bond is made and broken.
Read βChemistry of the SβS bond, connectivity problems, cystine knots, oxidative folding and handling cysteine peptides.
Read βWhy cyclisation works, how rings are closed, natural cyclic peptides, and macrocycles as drugs.
Read βMass shifts of the common modifications, amidation, phosphorylation, lipidation, and artefacts.
Read βHelices, Ξ²-hairpins and disorder in short peptides, helix propensity, and measuring structure by CD.
Read βChirality, D-residues in nature and in drugs, mirror-image peptides, and how to detect them.
Read βCharge, amphipathicity and the helical wheel, how AMPs kill bacteria, selectivity and resistance.
Read βHow peptides are made, purified, analysed, sequenced, stored and handled in the laboratory.
How SPPS works, Fmoc vs Boc chemistry, resins, coupling reagents and difficult sequences.
Read βReversed-phase separation, TFA ion pairing, scaling up, and what a 95% purity figure really means.
Read βESI and MALDI, tandem MS, and how to read b and y fragment ions, with a worked example.
Read βHow N-terminal sequencing works, why read length is limited, and how it compares with mass spectrometry.
Read βDegradation pathways, how to store and dissolve peptides, and how to avoid losses in the lab.
Read βDetailed profiles of individual peptides: structure, biology, history and the numbers behind them.
Two chains, three disulfides: discovery, biosynthesis from proinsulin, hexamers, and engineered analogues.
Read βTwo nine-residue hormones differing at two positions: structure, receptors, evolution and analogues.
Read βThe cellβs main thiol: the Ξ³-glutamyl bond, the GSH/GSSG redox couple, detoxification and lab uses.
Read βThe main peptide of bee venom: sequence, kinked helix, membrane lysis, and melittin in research.
Read βHistidine dipeptides of muscle: Ξ²-alanine, pH buffering, species differences and Ξ²-alanine supplementation.
Read βCone snail venom peptides: disulfide frameworks, ion channel targets, ziconotide and Ξ±-conotoxin isomers.
Read βThe first neuropeptide found: tachykinins, pain and inflammation, NK1 antagonists and Met oxidation.
Read βReninβangiotensin and kinin systems, how ACE links them, and the snake venom origin of captopril.
Read βEnkephalins, endorphins and dynorphins: the YGGF motif, three precursors, and what endorphins are not.
Read βHuman host defence peptides: defensin disulfide classes, LL-37, salt sensitivity and immune signalling.
Read βA lantibiotic food preservative: thioether rings, lipid II binding, and why calculators cannot handle it.
Read βThe dipeptide sweetener: why the methyl ester matters, how it degrades, and peptides in taste.
Read β