Compound Guides

GHK-Cu: A Research Guide to the Copper Tripeptide Complex

What GHK-Cu is structurally, the measured copper-binding constants, the fibroblast and cell-free assays it has actually been studied in, and the questions the primary literature leaves open after fifty years.

Glutathione (GSH): Structure, Enzymology, and How Its Redox State Is Measured

Glutathione is not a signaling peptide — it is the most abundant low-molecular-weight thiol cells synthesize. A guide to its biosynthesis, the three enzyme families that require it, the Nernst arithmetic behind GSH/GSSG, and what the literature still does not know.

IGF-1 LR3: A Research Guide

IGF-1 LR3 is native IGF-I carrying a 13-residue N-terminal extension and arginine in place of Glu3 — 83 residues in total. Its extra potency is not receptor affinity: in a cell line with no detectable binding proteins it was less potent than IGF-I. What has been measured, and why no identity block is published.

Kisspeptin-10: KISS1R Pharmacology, Assay Systems and Stability — Research Guide

Kisspeptin-10 is the amidated C-terminal decapeptide of the KISS1 gene product. This guide covers its verified identity, its receptor pharmacology as measured in recombinant and neuronal systems, the assay readouts behind those measurements, and the proteolytic and thermal instability the literature documents.

Melanotan II (MT-2): A Research Guide

Melanotan II is a cyclic lactam analog of alpha-MSH designed in 1989 to lock a flexible hormone fragment into one conformation. It binds four of the five melanocortin receptors, which makes it a powerful reference ligand and a poor subtype probe. What has been measured, in which systems, and where the record stops.

MOTS-c: A Research Guide to the Mitochondrial 12S rRNA-Encoded Peptide

MOTS-c is a 16-residue peptide encoded in a short open reading frame inside the mitochondrial 12S rRNA gene. This guide covers its verified identity data, the folate-cycle/AMPK and CK2 mechanisms as actually studied, the model systems involved, and — at equal length — what the literature does not establish.

Selank: A Research Guide

Selank is tuftsin plus a Pro-Gly-Pro tail. This guide separates what has been measured — tritiated GABA binding in membrane preparations, IPSCs in rat hippocampal slices, serum peptidase inhibition at 20 μM, plasma degradation fragments — from what the literature never established, including any receptor of its own.

Semax (MEHFPGP): A Research Guide to Its Identity, Binding Site and Preclinical Record

Semax is a synthetic heptapeptide joining the ACTH(4-7) fragment to a C-terminal Pro-Gly-Pro extension. This guide covers its verified identity data, the nanomolar calcium-dependent binding site measured in rat forebrain membranes, the assay readouts it has been studied with, and the gaps left open.

Sermorelin (GRF 1–29 NH₂): Receptor Pharmacology, Model Systems and What the Literature Does Not Establish

Sermorelin is the amidated N-terminal 29 residues of human GHRH. This guide covers its verified identity, the GHRHR cloning and cryo-EM work behind its mechanism, the alanine-scan and binding SAR, the specific cell and membrane systems it has been examined in, and the sizeable gaps that remain.

SS-31 (Elamipretide): Research Guide

SS-31 (elamipretide) is a cationic aromatic tetrapeptide studied for its partitioning into cardiolipin-containing membranes. This guide covers verified identity data, the biophysical and proteomic evidence for its mechanism, the model systems it has actually been examined in, and what the literature does not establish.

Tesamorelin: A Research Guide

Tesamorelin is hGRF(1-44)NH2 with a single trans-3-hexenoyl group on Tyr1. This guide covers its verified identity, what the GHRH receptor literature actually establishes, the narrow set of systems the analog itself has been examined in, and the receptor-level data that has never been published.

CJC-1295 (no DAC) + Ipamorelin: Two Peptides, Two Receptors, One Vial

A blend has no molecular identity, so this guide publishes no CAS or formula — and explains why. It separates what the literature establishes about the GHRH receptor and GHS-R1a from what has only been assumed about the pair, including a naming inconsistency that sends researchers to the wrong paper.

NAD+ (Nicotinamide Adenine Dinucleotide): A Research Guide

NAD+ is a dinucleotide, not a peptide, and it does two jobs that are usually discussed as one: a recycled hydride carrier, and a consumable substrate for sirtuins, PARPs, CD38 and SARM1. What has actually been measured, in which compartment, and why a flat whole-cell number can hide a collapsed mitochondrial pool.

PT-141 (Bremelanotide): A Research Guide

PT-141 (bremelanotide) is a cyclic lactam analog of alpha-MSH. This guide covers its verified identity, the melanocortin receptor pharmacology its scaffold has been characterized in, the cell systems it has been examined in, and the limits of the record — including a subtype panel that exists in one laboratory.

TB-500 (Ac-LKKTETQ): A Research Guide

TB-500 is the N-terminally acetylated 17–23 fragment of thymosin β4. Most of the biology attributed to it was measured on the unacetylated peptide or the full-length protein, and the one study that tested the acetylated form directly found no significant activity for it. What has been measured, and what has not.

Beta-Arrestin Recruitment Assays and Biased Agonism: BRET, Complementation, Imaging and Bias Factors

What a beta-arrestin recruitment assay physically measures across BRET, enzyme complementation and imaging formats, how a bias factor is calculated from transduction coefficients with the arithmetic and error propagation shown, and why the resulting number is a property of the assay system.

cAMP Accumulation Assays: What an EC50 From One Actually Means

An EC50 from a cAMP assay is not a property of the compound. It is that compound read through one receptor at one density, in one cell background, at one read time, with a phosphodiesterase inhibitor in the buffer. Gs coupling, IBMX, HTRF and Alpha formats, receptor reserve, and the arithmetic of amplification.

Cell Culture Practice for Peptide Experiments: Serum, Passage, Mycoplasma and Identity

A cell-based number describes a system, not a molecule. What serum binding, labware adsorption, medium chemistry, passage drift, mycoplasma and cell line identity each do to a peptide result — with the arithmetic worked, and the difference between evidence and convention stated.

Dose-Response Curves: EC50, IC50 and the Hill Slope

An EC50 is a parameter of a fitted curve, not a measurement. This guide covers four-parameter logistic fitting, what a Hill slope away from unity indicates, how to read a confidence interval on potency, and why comparing EC50 values across papers is usually invalid.

ELISA for Peptide Quantification: Cross-Reactivity and Matrix Effects

An ELISA measures immunoreactivity, not molar concentration. This guide covers what separates the two for peptides: sandwich versus competitive formats, epitope availability, cross-reactivity with fragments and precursors, matrix interference, and standard curve design.

Radioligand Binding Assays: Kd, Bmax and Competition

A binding constant is a subtraction between two counts, on a system assumed to be at equilibrium, at a concentration assumed to be the one on the tube. How saturation and competition differ, what the nonspecific blank removes, why Cheng-Prusoff is an approximation, and why incubations are too short.

Reading a Dose-Response Figure Critically

A dose-response curve makes three separable claims, and each can fail on its own. What n actually counts, which statistic the error bars show, how the choice of 100% moves the plateaus, what a truncated axis magnifies, and why a curve without a top plateau reports an EC50 that was never measured.

Receptor Selectivity Panels: What a Clean Profile Does and Does Not Show

A panel of "no significant activity" entries is a bounded negative, not proof of specificity. This guide works through panel composition, the arithmetic linking single-point percent inhibition to IC50, how hit thresholds are chosen, and why a selectivity ratio depends on which value is the denominator.

Western Blot for Signaling Readouts: Phospho-Specific Antibodies, Normalization, and the Limits of Densitometry

A phospho-blot reports antibody retained on a membrane, not a signaling state. This guide covers how phospho-specific antibodies are validated, why loading controls are themselves measurements, how to establish a linear range from a dilution series, and the arithmetic showing what saturation does to a fold change.

Isothermal Titration Calorimetry: Binding Thermodynamics

An ITC instrument measures heat and nothing else; every other number on the report is a fitted parameter. What the c-value window is really a proxy for, why the buffer owns part of the measured enthalpy, how cell and syringe concentration errors propagate differently, and how compensation gets manufactured.

LC-MS/MS Proteomics: From Digest to Identification

A peptide identification is not an observation. It is the best-scoring candidate among the sequences the search was permitted to consider. What the digest commits you to, why CID and ETD give different ladders, what a target-decoy false discovery rate estimates, and which denominator it uses.

Pipetting Accuracy and Volumetric Error in Serial Dilutions

A dilution series is a chain of multiplications, so a 2% short transfer repeated six times is not a 2% error but an 11.5% one. Systematic versus random error, how each propagates, what gravimetric and photometric verification actually establish, and how a small tip error becomes a large potency error.

Statistics for Bench Experiments: Power, Effect Size and Multiple Comparisons

A p-value is not the probability a result is real, an n of 3 is not a sample size, and a correction chosen after seeing the data is not a correction. What a p-value measures, why n = 3 needs a three-standard-deviation effect for 80% power, what counts as an independent replicate, and how the corrections differ.

Buffers and pH Control in Peptide Experiments

A buffer is a reagent in large molar excess, not a background condition. What the pKa on the bottle omits, how fast capacity falls away from it, why 50 mM phosphate carries 2.2 times its nominal ionic strength, which buffers bind metals or make peroxide, and the ionization enthalpy calorimetry cannot ignore.

Cell Viability and Cytotoxicity Assays in Peptide Work: What MTT, ATP, LDH and Live/Dead Actually Measure

MTT, ATP luminescence, LDH release and live/dead staining each measure a different physical quantity, and none of them measures viability. What each format is sensitive to, the two classes of tetrazolium artifact, the peptide-specific formazan trafficking confound, and why a viability drop is not a mechanism.

Controls in Peptide Assays: What Each One Actually Rules Out

Vehicle, scrambled sequence, inactive analog, receptor-null cells, positive reference agonist: each closes off one specific alternative explanation and is silent about the rest. This guide states, for every control in the standard set, the artifact it excludes and the artifact it leaves entirely untouched.

Fluorescent Labeling of Peptides: FITC, TAMRA and Cyanine Chemistries

A fluorescent label is a second molecule bolted to the first, carrying its own charge, mass and photochemistry. FITC, TAMRA and cyanine chemistries, how an attachment site is chosen, what quenching and photobleaching remove, and the case where moving the label changed the answer by up to two orders of magnitude.

In Vitro Permeability Models: Caco-2, PAMPA and Transport Assays

An apparent permeability is a flux divided by a concentration that was assumed, across an area that was nominal, through a barrier the laboratory built. What Caco-2 and PAMPA each represent, how Papp and efflux ratios are computed, which controls decide whether a plate is reportable, and where extrapolation stops.

Molecular Docking and In Silico Prediction for Peptides: What a Score Is Not

A docking score is a pose-selection statistic reported in energy-like units, not an affinity. Why peptide flexibility breaks small-molecule docking assumptions, what the published protein-peptide benchmarks actually report, how pose quality is measured, and what it takes to validate a prediction.

Peptide Sequence Bioinformatics: UniProt, BLAST and Alignment

A sequence is a string of letters, but every number attached to it depends on a convention the string does not carry. Canonical sequences and isoforms, the precursor-versus-mature offset that silently shifts residue positions, why short queries defeat default search settings, and how to read a percent identity.

Reproducibility in Peptide Research: Where Results Fail to Replicate

Most replication failures are not fraud; they are experiments that were not the experiment the methods section described. Where the discrepancies hide: reagent identity, cell line misidentification, undisclosed peptide content, pseudoreplication and low power, and the reporting that closes each gap.

Surface Plasmon Resonance for Peptide Binding Kinetics

SPR reports a refractive index change; every rate constant is inferred from it under a model you chose. Immobilization chemistry and orientation, ka and kd and the KD they define, mass transport limitation, regeneration, and the arithmetic that makes a small analyte hard.

Cell Uptake of Peptides: Endocytosis, Translocation and How Each Is Distinguished

Cell-associated, internalized and cytosol-accessible are three different measurements. The fixation artifact that overturned an early literature, what clathrin, caveolar and macropinocytic assignments rest on, why low-temperature and inhibitor controls are necessary but not sufficient, and the arithmetic behind them.

Membrane Mimetics: Liposomes, Bicelles and Nanodiscs

Every membrane measurement made outside a cell is made in a substitute. Lipid composition and curvature, the q ratio that drifts when you dilute it, scaffold length as a size control, detergent-free polymer extraction, and what each construct throws away.

NMR for Peptide Structure in Solution

Solution NMR measures frequencies and intensities, not coordinates. NOE distance bounds and their spin-diffusion bias, chemical shift indexing and its limits, why inverse-sixth-power averaging lets a minority conformation dominate a restraint, and why a bundle of models reports precision, not motion.

Plasma and Serum Stability Assays for Peptides

A plasma stability half-life is a narrower number than it looks. This guide covers matrix choice, the protease classes doing the cutting, anticoagulant and quench chemistry, half-life fitting, and why species, donor and dilution change the answer.

Protease Specificity: Which Enzymes Cut Where

Exopeptidases need a free terminus, endopeptidases do not — yet neprilysin still counts from the C-terminus. A guide to subsite nomenclature, the DPP-4 and neprilysin structures behind their preferences, and how cleavage sites are mapped by PICS, MSP-MS and N-terminomics.

Receptor Internalization and Trafficking Assays

An internalization assay measures accessibility, not location. Surface biotinylation and antibody labeling, pH-sensitive fluorophores and the pulsed-pH protocol, separating recycling from degradation, and the dependencies hidden in any internalization percentage — starting with which quantity is the denominator.

SEC-MALS and Analytical Ultracentrifugation for Oligomeric State

A retention time is a hydrodynamic property, not a mass, and the calibration curve converting one to the other carries every assumption of the standards. What light scattering fixes, what it does not, how sedimentation velocity separates with no column at all, and how to tell a stable oligomer from a reversible one.

Thermal Shift Assays: DSF, nanoDSF and What a Tm Shift Means

A thermal shift assay reports the temperature at which a fluorescence signal changes most steeply. Dye-based DSF versus intrinsic-fluorescence nanoDSF, what a melting temperature does and does not report, why a Tm shift is not a binding affinity, and where buffer screening holds up.

Alanine Scanning and Binding Hotspots: What One Substitution Actually Reports

An alanine scan returns positions and free-energy numbers, but those numbers are differences between two molecules under one set of conditions, not properties of residues. What C-beta truncation removes, how the O-ring hotspot picture was built, where additivity fails, and why deletion is a different experiment.

Half-Life Extension Chemistry for Peptides

Two mechanisms sit under every half-life platform: added hydrodynamic bulk and FcRn recycling. Albumin-binding fatty acids, albumin and Fc fusion, PASylation and XTEN, and glycoengineering, with what each costs in receptor affinity, valency, expression system and manufacturability.

Peptide Conjugates: Linker Chemistry and Payload Release

Cleavable versus non-cleavable is a statement about catabolic fate, not bond strength. What actually cleaves a valine-citrulline linker, why a mouse esterase broke a whole class of stability data, how an average drug-to-peptide ratio hides its distribution, and what a stability assay is really measuring.

Antimicrobial Peptide Screening: MIC, Hemolysis and Selectivity

A MIC is a property of a peptide in one medium, against one inoculum, in one kind of plastic. Broth microdilution and its two-fold ladder, divalent cations and salt, inoculum dependence, the hemolysis assay's moving denominator, and why a selectivity index does not survive the trip between papers.

Cell-Penetrating Peptide Design and Its Controls

Cationic versus amphipathic classes, why cargo and fluorophore are part of the molecule, what the scrambled and D-enantiomer controls can and cannot decide, and the assays that measure cytosolic arrival rather than uptake.

Cryo-EM of Peptide-Receptor Complexes: What a Map Establishes

A cryo-EM structure is a map inferred from noisy images, then a model inferred from that map. The single-particle workflow, why the global resolution figure is a half-set statistic, how resolution varies within one map, map-to-model fitting and scoring, and what a deposited GPCR complex actually establishes.

mRNA Display and Ribosome Display: Covalent Linkage, Cell-Free Libraries, and What Each Buys Over Phage

Puromycin makes the genotype-phenotype link covalent; ribosome display holds it together with buffer conditions instead. What that difference costs, where cell-free library sizes actually come from, why fusion yield depends on flanking sequence, and which phage artifacts these formats remove.

Peptide Microarrays and Epitope Mapping

An overlapping scan measures one intensity per spot and nothing else. Scan arithmetic and what the offset guarantees, SPOT synthesis on cellulose, why linear peptides cannot hold a conformational epitope, what spot intensity does and does not report, and the controls that separate binding from surface chemistry.

Radiolabeled Peptides: Chelators, Specific Activity and Radiochemical Purity

Molar activity and radiochemical purity have different denominators, and neither converts into the other. Matching a bifunctional chelator to the radiometal, trace metals competing for the cage, radiolysis after synthesis, and the layered QC a labeled batch actually receives.

How to Read a Peptide Structure-Activity Relationship Table

A SAR table looks like a ranking but is a set of measurements. What a fold-change column is a ratio of, why potency, affinity and efficacy can point in different directions, how far apart two correct EC50 values can sit, and what happens to a series when the readout changes.

X-Ray Crystallography of Peptide-Protein Complexes

A crystal structure is a model refined against diffraction data, and the bound peptide contributed least to it. What a resolution figure permits, why global R factors will not catch a bad peptide, what B-factors and occupancies encode, and how a peptide can be genuinely bound yet only partly supported by density.

Fluorescence Polarization and Anisotropy in Peptide Binding Assays

A polarization reading reports how far a fluorophore rotated during its excited-state lifetime, and binding is only one reason that number moves. Why the tracer must be the small partner, how probe choice sets the affinity floor, why Cheng-Prusoff is the wrong conversion in competition mode, and the artefacts that shift mP without shifting occupancy.

Biolayer Interferometry for Peptide Binding Kinetics

BLI reports the optical thickness of a layer at a fibre tip as a wavelength shift in nanometres; every rate constant after that is inference. What the dip-and-read format changes about loading, referencing, mass transport and rebinding compared with SPR, and why fast-off peptide interactions defeat it.

Microscale Thermophoresis and the Limits of an MST Binding Constant

How an MST trace is built from a temperature jump, directed migration and re-equilibration, and how label chemistry, detergent, capillary adsorption and aggregation get into the number. Written for deciding what an MST Kd licenses next to ITC and SPR.

Hydrogen-Deuterium Exchange MS: EX1, EX2 and Protection Differences

How amide backbone exchange chemistry, the EX1 and EX2 regimes, quench conditions and back-exchange set the limits of an HDX-MS dataset. Includes why a peptide that takes up less deuterium on ligand binding is not thereby a binding site.

Crosslinking Mass Spectrometry and the Limits of a Crosslink

A crosslink is a proximity measurement with an upper bound, not an interaction. This guide covers crosslinker chemistry and spacer arms, the quadratic search problem, false discovery rate estimation at spectrum, residue-pair and protein-pair level, and the Calpha-Calpha bounds that turn a hit into a restraint.

Calcium Flux Assays for Gq Receptors and the Non-Equilibrium Problem

How a Gq calcium transient is generated, read and mis-read: indicator chemistry and buffering, dye loading and anion-transport blockers, peak versus area under the curve, promiscuous and chimeric Galpha subunits, and receptor reserve. Written for deciding what a calcium EC50 does and does not license.

Ion Mobility Mass Spectrometry of Peptide Conformers

How drift-tube, travelling-wave and trapped ion mobility turn an arrival time into a collision cross section, what a CCS distribution licenses you to conclude about gas-phase conformer populations, and where that conclusion stops short of solution structure.

Time-Resolved FRET and Lanthanide Homogeneous Proximity Assays

A TR-FRET reading says two labels came close, not how close. What the lanthanide donor and the time gate actually suppress, what the two-wavelength ratio is licensed to correct, why the r^-6 dependence makes this proximity rather than distance, and the hook that leaves one sandwich reading ambiguous.

Molecular Dynamics for Peptide Conformational Sampling

An MD ensemble is a force field's prediction, not a measurement. Known force-field biases for disordered and helical peptides, what implicit solvent trades away, the gap between accessible simulation time and the process you care about, what a free-energy surface from replica exchange, metadynamics or umbrella sampling does and does not establish, and how far agreement with NMR, order-parameter and CD data actually gets you.

Fluorogenic and FRET Peptide Substrates for Protease Kinetics

A donor and a quencher flanking the scissile bond report any cut between them; a coumarin leaving group reports one bond and carries no prime side. How the inner filter effect caps your substrate titration, why kcat/KM is often the only constant you can honestly report, and which controls decide whether the trace means anything.

Single-Molecule FRET for Peptide Conformational Dynamics

An ensemble FRET reading is one number that a two-state mixture and a homogeneous population produce alike. What a distribution of single-molecule efficiencies adds, where the Forster radius makes you blind, what site-specific double labelling costs in purification, how blinking and tethering can manufacture dynamics that are not there, and the controls that test whether they did, and why an uncorrected efficiency is only a proximity ratio.

Label-Free Cellular Assays: Impedance and Dynamic Mass Redistribution

Impedance and dynamic mass redistribution read a whole-cell rearrangement, not a pathway. What each sensor physically integrates, what the kinetic trace holds that an endpoint read discards, how selective inhibitors put pathway identity back in, and why adhesion, confluence and cell background can set the amplitude before the ligand does.

Patch Clamp for Peptide Ion Channel Modulators

Configuration decides which membrane face a peptide can reach; the voltage protocol decides whether a gating shift is visible at all; series resistance error and adsorptive loss can decide whether the resulting numbers mean anything. What each measurement licenses, and what it does not.

Biosensor Immobilisation Chemistry and Ligand Density

Amine coupling does not choose which residue attaches, and when the reactive residue sits close to the binding determinant, that can cost activity. This guide covers electrostatic preconcentration and the pH scout that finds it, thiol and capture chemistries, how ligand density shapes the constants you report, the flow-rate test for mass transport limitation, regeneration scouting, and reference-surface design.

AlphaFold for Peptides: Reading Confidence, and Its Limits

A predicted structure is a hypothesis with a confidence array attached. What pLDDT and PAE each license you to conclude, why low confidence on a short peptide often reports disorder rather than failure, the alignment-depth problem for peptides and designed sequences, and what a model containing no ligand, ion, modification or membrane cannot settle.

Solid-State NMR of Peptide Fibrils and Assemblies

A fibril has no solution spectrum and no diffraction-quality crystal. What magic-angle spinning and dipolar recoupling put back, how segmental, sparse, diluted and mixed labelling each answer a different question, how parallel in-register is told from antiparallel, and why the structure you obtain belongs to the preparation that produced it.

Thioflavin T Kinetics for Aggregation Assays

The dye lights up when an aromatic groove holds its rings in the right electronic environment, on fibrils a groove spanning four consecutive beta-strands, which is why species without cross-beta architecture can be absent from the data rather than present at zero and why plateau heights compared across conditions are not a mass comparison. What the lag, growth and plateau phases actually contain, why global fitting across a concentration series is what recovers microscopic rate constants, and how agitation, read interval, surface area, the meniscus and dye concentration move the curve you are comparing.

Vesicle Dye Leakage Assays for Membrane-Active Peptides

A leakage curve reports dequenching, not mechanism. How ANTS/DPX requenching and single-vesicle imaging separate graded from all-or-none release, why lipid composition and lipid-to-peptide ratio dominate the result, and which osmotic and dye artefacts produce signal with no membrane event behind them.

Small-angle X-ray scattering: what a solution curve licenses

A solution SAXS measurement is one dimension of data. This is what Guinier, P(r), Porod and Kratky analysis extract from it, the point at which each stops being valid, and why a single ab initio envelope is a weak claim.

Coarse-Grained Simulation of Peptide Assembly with MARTINI

A MARTINI trajectory answers a narrow question well. What the 4-to-1 mapping buys in reach and costs in chemical detail, why the backbone bead's secondary structure is an input rather than a prediction, how large the encoding choice can make an aggregation score swing, why effective microseconds are not experimental microseconds, the documented over- and under-aggregation biases and the corrections aimed at them, and when a coarse-grained morphology has to be backmapped before it means anything.

Peptide Pull-Downs: Bait Design, Controls and Enrichment Ratios

An immobilised peptide bait recovers weak motif interactions because it is presented at a high local concentration, and that same crowding can supply avidity. This guide covers anchoring direction and spacer, bait density, lysate and wash conditions, the sequence controls a beads-only channel cannot replace, on-bead versus eluted digestion, and the narrow claim an enrichment ratio supports.

Isothermal Chemical Denaturation and Peptide Stability

Chemical denaturation swaps temperature for denaturant as the stability axis. What m-values report about buried surface, what the extrapolation to zero denaturant assumes, how reversibility is demonstrated, why probes disagree, and where short peptides defeat the two-state model.

Sequence-Based Secondary Structure Prediction for Peptides

Propensity tables, profile-based predictors and disorder scores each summarise a sequence in a different way, and the accuracy figures they carry were measured on folded proteins. What a per-residue prediction licenses for a designed or short peptide, why the helical wheel is a design tool rather than evidence, and how circular dichroism and the chemical shift index settle the question.

NMR Chemical Shift Perturbation: Mapping a Binding Interface

Titrate an unlabelled partner into a labelled one and peaks move. How the combined shift is weighted and what it discards, what each exchange regime lets you measure, the concentration window in which a titration curve yields a valid Kd, and why a perturbation map is a hypothesis about the interface rather than a picture of it.

Peptide Metal Binding: Donor Sets, Constants and Methods

The terminal amine, deprotonated backbone amides, histidine imidazole, cysteine thiolate and aspartate or glutamate carboxylates are the donors a peptide brings to a metal ion. What that donor set fixes, why an affinity quoted without pH, buffer and competitor cannot be read, and what potentiometry, CD, EPR and mass spectrometry each establish.

Aggregation Prediction Algorithms from Sequence

Physicochemical and thermodynamic methods converge on the same aggregation-prone-region output while structure-based scoring asks a narrower question, and a per-residue score has no axis for the buffer you will actually use. What the published benchmarks establish for hexapeptide classification versus residue-level annotation of whole proteins, why the amyloid-specific question is narrower than the one you are asking, and how to use a propensity profile to rank candidates for the plate rather than to conclude.

Cyclic Peptide Conformational Analysis by Solution NMR

Cyclisation narrows the conformational distribution an NMR experiment averages over, but it does not guarantee a single conformer. What cis/trans exchange data, amide temperature coefficients, NOEs and residual dipolar couplings each license, and where a single fitted structure becomes a shape that is never populated.

Machine-Learned Peptide Property Prediction: What an AUC Licenses

A benchmark AUC describes the ordering of one curated set under one choice of negatives; it is not a probability that your designed sequence has the property. What one-hot encodings, physicochemical descriptors and protein language model embeddings can each carry for a 12-mer, why random splits leak through sequence similarity, what the negative-sampling result does to published AMP benchmark analyses, and how to report an applicability-domain distance so a score can be read at all.

Cyclic Peptide Passive Permeability and Molecular Chameleonicity

Permeability in this class tracks how many backbone donors are still exposed at the membrane rather than how many the molecule owns, though no single count settles it. The size and polarity boundaries, the intramolecular hydrogen bonding that shields donors in a low dielectric, how the two conformations are demonstrated by NMR in polar and apolar solvent, N-methylation as the designed alternative, and why PAMPA and cell monolayers disagree.

Predicting Protease Cleavage Sites From Sequence

Sequence-based predictors return a ranked list of scissile bonds, not a verdict. What the subsite matrices encode, why coverage in the underlying cleavage databases is so uneven, where structural accessibility breaks a sequence-only score, and how LC-MS of the actual digest settles the question.

Hydrogen Bond and Salt Bridge Analysis in Peptide Structures

Contact counts are conditional on the cutoffs that produced them, so they do not transfer between programs or between papers. Why hydrogen bond and salt bridge definitions disagree by construction, what trajectory occupancy adds and what it inherits from the force field, why a buried charge pair can be stabilising or destabilising depending on desolvation cost, and what amide temperature coefficients, hydrogen exchange and double-mutant cycles each actually license you to conclude.

Proving Allosteric Modulation in Peptide Receptor Assays

A saturable, probe-dependent effect is what separates a modulator from a competitor. This guide covers the cooperativity factor alpha and the ceiling it sets in a binding curve, the operational model of allosterism, probe dependence as both diagnostic and complication, the radioligand dissociation experiment a competitor cannot pass, how to rule out receptor reserve and allosteric agonism, and the extracellular surfaces a peptide ligand can actually reach.

BPC-157 in Research: Overview

A research overview of BPC-157, a synthetic stable pentadecapeptide studied in vitro for cytoprotection, fibroblast and collagen activity, and VEGF/NO angiogenesis signaling.

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All guides

GHK-Cu: A Research Guide to the Copper Tripeptide Complex

Glutathione (GSH): Structure, Enzymology, and How Its Redox State Is Measured

IGF-1 LR3: A Research Guide

Kisspeptin-10: KISS1R Pharmacology, Assay Systems and Stability — Research Guide

Melanotan II (MT-2): A Research Guide

MOTS-c: A Research Guide to the Mitochondrial 12S rRNA-Encoded Peptide

Selank: A Research Guide

Semax (MEHFPGP): A Research Guide to Its Identity, Binding Site and Preclinical Record

Sermorelin (GRF 1–29 NH₂): Receptor Pharmacology, Model Systems and What the Literature Does Not Establish

SS-31 (Elamipretide): Research Guide

Tesamorelin: A Research Guide

CJC-1295 (no DAC) + Ipamorelin: Two Peptides, Two Receptors, One Vial

NAD+ (Nicotinamide Adenine Dinucleotide): A Research Guide

PT-141 (Bremelanotide): A Research Guide

TB-500 (Ac-LKKTETQ): A Research Guide

Beta-Arrestin Recruitment Assays and Biased Agonism: BRET, Complementation, Imaging and Bias Factors

cAMP Accumulation Assays: What an EC50 From One Actually Means

Cell Culture Practice for Peptide Experiments: Serum, Passage, Mycoplasma and Identity

Dose-Response Curves: EC50, IC50 and the Hill Slope

ELISA for Peptide Quantification: Cross-Reactivity and Matrix Effects

Radioligand Binding Assays: Kd, Bmax and Competition

Reading a Dose-Response Figure Critically

Receptor Selectivity Panels: What a Clean Profile Does and Does Not Show

Western Blot for Signaling Readouts: Phospho-Specific Antibodies, Normalization, and the Limits of Densitometry

Isothermal Titration Calorimetry: Binding Thermodynamics

LC-MS/MS Proteomics: From Digest to Identification

Pipetting Accuracy and Volumetric Error in Serial Dilutions

Statistics for Bench Experiments: Power, Effect Size and Multiple Comparisons

Buffers and pH Control in Peptide Experiments

Cell Viability and Cytotoxicity Assays in Peptide Work: What MTT, ATP, LDH and Live/Dead Actually Measure

Controls in Peptide Assays: What Each One Actually Rules Out

Fluorescent Labeling of Peptides: FITC, TAMRA and Cyanine Chemistries

In Vitro Permeability Models: Caco-2, PAMPA and Transport Assays

Molecular Docking and In Silico Prediction for Peptides: What a Score Is Not

Peptide Sequence Bioinformatics: UniProt, BLAST and Alignment

Reproducibility in Peptide Research: Where Results Fail to Replicate

Surface Plasmon Resonance for Peptide Binding Kinetics

Cell Uptake of Peptides: Endocytosis, Translocation and How Each Is Distinguished

Membrane Mimetics: Liposomes, Bicelles and Nanodiscs

NMR for Peptide Structure in Solution

Plasma and Serum Stability Assays for Peptides

Protease Specificity: Which Enzymes Cut Where

Receptor Internalization and Trafficking Assays

SEC-MALS and Analytical Ultracentrifugation for Oligomeric State

Thermal Shift Assays: DSF, nanoDSF and What a Tm Shift Means

Alanine Scanning and Binding Hotspots: What One Substitution Actually Reports

Half-Life Extension Chemistry for Peptides

Peptide Conjugates: Linker Chemistry and Payload Release

Antimicrobial Peptide Screening: MIC, Hemolysis and Selectivity

Cell-Penetrating Peptide Design and Its Controls

Cryo-EM of Peptide-Receptor Complexes: What a Map Establishes

mRNA Display and Ribosome Display: Covalent Linkage, Cell-Free Libraries, and What Each Buys Over Phage

Peptide Microarrays and Epitope Mapping

Radiolabeled Peptides: Chelators, Specific Activity and Radiochemical Purity

How to Read a Peptide Structure-Activity Relationship Table

X-Ray Crystallography of Peptide-Protein Complexes

Fluorescence Polarization and Anisotropy in Peptide Binding Assays

Biolayer Interferometry for Peptide Binding Kinetics

Microscale Thermophoresis and the Limits of an MST Binding Constant

Hydrogen-Deuterium Exchange MS: EX1, EX2 and Protection Differences

Crosslinking Mass Spectrometry and the Limits of a Crosslink

Calcium Flux Assays for Gq Receptors and the Non-Equilibrium Problem

Ion Mobility Mass Spectrometry of Peptide Conformers

Time-Resolved FRET and Lanthanide Homogeneous Proximity Assays

Molecular Dynamics for Peptide Conformational Sampling

Fluorogenic and FRET Peptide Substrates for Protease Kinetics

Single-Molecule FRET for Peptide Conformational Dynamics

Label-Free Cellular Assays: Impedance and Dynamic Mass Redistribution

Patch Clamp for Peptide Ion Channel Modulators

Biosensor Immobilisation Chemistry and Ligand Density

AlphaFold for Peptides: Reading Confidence, and Its Limits

Solid-State NMR of Peptide Fibrils and Assemblies

Thioflavin T Kinetics for Aggregation Assays

Vesicle Dye Leakage Assays for Membrane-Active Peptides