Protein Labeling Calculator Protein Labeling Calculator Accurately calculate the amount of labeling reagent (NHS-ester dyes, biotin, fluorescent tags, etc.) needed for your protein based on established bioconjugation chemistry. Protein Molecular Weight (kDa) Protein Concentration (mg/mL) Reaction Volume (µL) Labeling Reagent MW (Da) Desired Dye-to-Protein Ratio (D/P) 1 : 12 : 13 : 14 […]
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Photo-Crosslinking Calculator Calculate Photo-Crosslinking Parameters Photo-Crosslinker Type Sulfo-SANPAH (NHS-aryl azide)BS3 + UV (for diazirine testing)Benzophenone (BP)Aliphatic Diazirine (long-lived carbene)Sulfo-SDA (NHS-diazirine)LC-SDA (long-chain diazirine)ABDAN (azide-benzophenone dual) Crosslinker Concentration (mM) Reaction Volume (µL) Molecular Weight of Crosslinker (g/mol) Auto-filled based on selected crosslinker UV Exposure Time (minutes) UV Wavelength (nm) 254 nm (aryl azide optimal)302 nm (general)365 nm
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Chemical Crosslinking Calculator Calculate Exact Crosslinker Amounts Accurate stoichiometry for protein-protein, protein-peptide, hydrogel, and polymer crosslinking Protein / Polymer Molecular Weight (kDa) Protein Concentration (mg/mL) Crosslinker Type BS3 / BS³ (Bis[sulfosuccinimidyl] suberate) – 572.43 DaDSS (Disuccinimidyl suberate) – 368.34 DaEDC + NHS (1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide + NHS) – Zero-lengthGlutaraldehyde (25% aqueous) – PolymericBS(PEG)5 – 572.5
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Protein Crosslinking Calculator Calculate Maximum Crosslinking Distance & Compatible Residue Pairs Select Crosslinker BS³ (Bis[sulfosuccinimidyl] suberate) – 11.4 ÅDSS (Disuccinimidyl suberate) – 11.4 ÅEDC (Zero-length, carbodiimide) – 0 ÅBS²G (Bis[sulfosuccinimidyl] glutarate) – 7.7 ÅDSSO (Disuccinimidyl sulfoxide) – 10.3 Å (cleavable)DSSO (MS-cleavable signature) – 10.3 ÅPDA (Pyridyl dithiol) – 13.0 ÅSulfo-SMCC (Heterobifunctional) – 11.6 ÅCustom Distance
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Cysteine Bridge Calculator Cysteine Bridge Calculator is a free, scientifically accurate online tool that predicts the number of possible disulfide bonds (cysteine bridges) in a protein or peptide from its amino acid sequence. Disulfide bonds formed between cysteine residues are critical for tertiary and quaternary protein structure stability. Cysteine Bridge Calculator Enter your protein/peptide sequence
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Disulfide Bond Calculator Enter Your Protein Sequence Only show cysteines that can realistically form disulfide bonds (≥10 residues apart) Show all possible Cys–Cys pairs (including very close ones) Calculate Disulfide Bonds Clear About the Disulfide Bond Calculator The Disulfide Bond Calculator is a free, accurate, and scientifically validated online tool that instantly identifies all cysteine
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Salt Bridge Network Calculator Free Online Salt Bridge Network Strength & Stability Calculator Calculate interaction energy, stability contribution, and network score of salt bridges in proteins and supramolecular systems. Positive Residue (Cation) Lysine (LYS)Arginine (ARG)Histidine (HIS) Negative Residue (Anion) Aspartic Acid (ASP)Glutamic Acid (GLU) Distance between charged groups (Å) pH of Environment Ionic
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Hydrogen Bonding Network Calculator Enter Protein Sequence & Hydrogen Bond Parameters Protein Sequence (single-letter code) Spaces, numbers, and lowercase will be ignored Max Donor–Acceptor Distance (Å) Standard: 3.0–3.5 Å (Pauling, 1960; Baker & Hubbard, 1984) Min D–H···A Angle (°) Commonly ≥120°–130° for strong H-bonds Display Mode Contact Map Style (2D Matrix)Network Graph (Force-Directed) Calculate Hydrogen
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Residue Interaction Calculator Calculate Amino Acid Residue Interaction Energy Based on peer-reviewed statistical potentials (2024–2025) Residue 1 Select ResidueAlanine (ALA)Arginine (ARG)Asparagine (ASN)Aspartic acid (ASP)Cysteine (CYS)Glutamine (GLN)Glutamic acid (GLU)Glycine (GLY)Histidine (HIS)Isoleucine (ILE)Leucine (LEU)Lysine (LYS)Methionine (MET)Phenylalanine (PHE)Proline (PRO)Serine (SER)Threonine (THR)Tryptophan (TRP)Tyrosine (TYR)Valine (VAL) Residue 2 Select ResidueAlanine (ALA)Arginine (ARG)Asparagine (ASN)Aspartic acid (ASP)Cysteine (CYS)Glutamine (GLN)Glutamic acid
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Protein Contact Map Calculator Enter or Paste Your Protein Sequence & Parameters Protein Sequence (single-letter code, no spaces & numbers will be removed) Distance Cutoff (Ångström) Common values: 6–12 Å (Cα–Cα) or 8 Å (Cβ–Cβ) Atom Pair for Contact Definition Cα – Cα (most common)Cβ – Cβ (recommended for side-chain contacts)Any heavy atom pair ≤
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