Nucleic acids naming for HADDOCK
Nucleic acids PDB file for HADDOCK should follow a three letter code naming for the various bases.
Supported nucleic acid bases:
  • ADE: Adenine
  • CYT: Cytosine
  • GUA: Guanidine
  • THY: Thymidine
  • URI: Uridine
Note that HADDOCK-compliant nucleic acid PDBs can be generated with our 3D-DART web server.
Modified amino acids and co-factors recognized by HADDOCK
All supported modified amino acids are in this list. Other modified amino acids are not supported.
For co-factors, parameters are automatically obtained from the PRODRG server, unless they are in this list.
Amino acids must be defined in the PDB file using ATOM lines, co-factors using HETATM lines.
Modified amino acids:
  • ASH: protonated ASP.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,OD1,OD2,HD2,C,O

  • DDZ: 3,3,-dihydroxy ALA.
    Atoms:
    N,HN,CA,HA,CB,HB1,OG1,HG1,OG2,HG2

  • GLH: protonated GLU.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,OE1,OE2,HE2,C,O

  • CYM: CYS with MTSL grouped.
    Atoms:
    CAC,CAS,CAD,NAQ,OAH,HAA,CAR,CAA,CAB,CAI,CAO,CAJ,SAL
    N,HN,CA,HA,CB,HB1,HB2,SG,C,O

  • CSP: phosphorylated CYS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,SG
    P,O1P,O2P,O3P,C,O

  • CYF: CYS without the sulfur H (for coordinating metals).
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,SG,C,O

  • CFE: CYS with an iron sulfur cluster.
    HADDOCK will automatically search for closeby CYF residues and created bonds with the iron cluster
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,SG,FE1,SF1,FE2,SF2,C,O

  • NEP: NE phosphorylated HIS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,ND1,HD1,CD2,HD2,CE1,HE1,NE2
    P,O1P,O2P,O3P,C,O

  • ALY: Acetylated LYS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
    NZ,HZ1,CZ,OZ,CM,HM1,HM2,HM3,C,O

  • MLZ: monomethyl LYS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
    NZ,HZ1,HZ2,CM3,HM31,HM32,HM33,C,O

  • MLY: dimethyl LYS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
    NZ,HZ1,HZ2,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O

  • M3L: trimethyl LYS.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,CE1,HE1,HE2
    NZ,HZ1,HZ2,CM1,HM11,HM12,HM13,CM2,HM21,HM22,HM23,CM3,HM31,HM32,HM33,C,O

  • HYP: 4R-hydroxyproline.
    Atoms:
    N,CA,HA,CB,HB1,HB2,CG,OG1,HG1,HG2,CD,HD1,HD2,C,O

  • PTR: O-Phosphotyrosine.
    Atoms:
    N,CA,C,O,OXT,CB,CG,CD1,CD2,CE1,CE2,CZ,OH,P,O1P,O2P
    O3P,1HN,2HN,HA,HXT,1HB,2HB,HD1,HD2,HE1,HE2,PHO2,PHO3

  • SEP: phosphorylated SER.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,OG
    P,O1P,O2P,O3P,C,O

  • TOP: phosphorylated THR.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,OG
    P,O1P,O2P,O3P,CG2,HG21,HG22,HG23,C,O

  • TYP or PTR: phosphorylated TYR.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH
    P,O1P,O2P,O3P,C,O

  • TYS: sulfonated TYR.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,CD1,HD1,CD2,HD2,CE1,HE1,CE2,HE2,CZ,OH
    S,O1S,O2S,O3S,C,O

  • ACE: N-terminal acetyl group.
    Atoms:
    CA,HA1,HA2,HA3,C,O

  • CTN: C-terminal amide group.
    Atoms:
    N,H1,H2


Co-factors:
  • HEB: Heme B
    Atoms: download an example PDB file

  • HEC: Heme C
    Atoms: download an example PDB file