Welcome to the Utrecht Biomolecular Interaction Web Portal >>

HADDOCK2.4 library



Supported carbohydrates
  • A2G: 2-N-acetyl-alpha-D-glucopyranose, different stereochemistry at C4
  • BGC: beta-D-glucopyranose
  • BMA: beta-D-mannopyronose
  • FCA: alpha-D-fucopyranose
  • FCB: beta-D-fucopyranose
  • FUC: alpha-L-fucopyranose
  • FUL: beta-L-fucopyranose
  • GAL (GLB): beta-D-galactopyranose
  • GLA: alpha-D-galactopyranose
  • GLC: alpha-D-glucopyranose
  • GXL: alpha-L-galactopyranose
  • MAG: 2-N-Acetyl-beta-D-glucopyranose + Methyl at O1
  • MAN: alpha-D-mannopyranose
  • NAG: 2-N-acetyl-beta-D-glucopyranose
  • NDG: 2-N-acetyl-alpha-D-glucopyranose
  • NGA: 2-N-acetyl-beta-D-galactopyranose
  • RAM: alpha-L-rhampyranose
  • SIA: alpha-N-acetyl neuraminic acid
  • SIB: beta-N-acetyl neuraminic acid
  • XYP: beta-D-xylopyranose
Carbohydrates should be provided with record HETAM, example: 
HETATM    9  C1  NAG B 102     171.992  99.750 236.168  1.00 10.00           C
Supported ions
  • AG: Silver
  • AL: Aluminium
  • AU: Gold
  • BR: Bromine
  • CA: Calcium
  • CD: Cadmium
  • CL: Chlore
  • CO: Cobalt
  • CR: Chromium
  • CS: Cesium
  • CU: Copper
  • F: Fluor
  • FE: Iron
  • HG: Mercury
  • HO: Holmium
  • I: Iodine
  • IR: Iridium
  • K: Potassium
  • KR: Krypton
  • LI: Adenine
  • MG: Magnesium
  • MN: Manganese
  • MO: Molybdenum
  • NA: Sodium
  • NI: Nickel
  • OS: Osmium
  • PB: Lead
  • PT: Platinum
  • SR: Strontium
  • U: Uranium
  • V: Vanadium
  • YB: Ytterbium
  • ZN: Zinc
Ions should be provided with their charge and a HETAM flag. Residue name should contain the absolute charge (e.g. ZN2) while atom name should have the exact charge (e.g. ZN+2), example: 
HETATM 3833 ZN+2 ZN2 A  42      21.391  -8.794  33.944  1.00 24.37          ZN
Supported multi atom ions
  • PO4: Phosphate
  • SO4: Sulphate
  • WO4: Tungstate
Supported co-factors:

The following will use HADDOCK's internal parameters, other co-factors will try to be automatically obtained from the PRODRG server.

Co-factors should be provided with record HETAM, example: 
HETATM    1  FE  HEB   500       3.565   0.487   0.949  1.00 15.00
Supported nucleic acid bases
    DNA
  • DA: Adenine
  • DC: Cytosine
  • DG: Guanidine
  • DT: Thymidine
    • RNA
  • A: Adenine
  • C: Cytosine
  • G: Guanidine
  • U: Uridine
Modified amino acids recognized by HADDOCK

All supported modified amino acids are in this list and must be defined as ATOM. Modified amino acids not present on this list are not supported.

Modified amino acids:

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

  • ASH: protonated ASP.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,OD1,OD2,HD2,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

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

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

  • CYC: special for covalent docking - vdw of Sulphur reduced.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,SG,C,O

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

  • 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

  • HY3: 3-hydroxyproline.
    Atoms:
    N,CA,HA,CB,OB1,HB1,HB2,CG,HG1,HG2,CD,HD1,HD2,C,O

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

  • 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

  • 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

  • MSE: Selenomethionine
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,CG,HG1,HG2,SE,CE,HE1,HE2,HE3,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

  • NME: C-terminal N-Methyl
    Atoms:
    N,HN,CA,HA1,HA2,HA3

  • PNS: Phosphopanthetine Serine.
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,OG,P,O1P,O2P,O3P,C,O,C28,H28,H29,C29,C30,H31,H32,H30,C31,H34,H35,H33,C32,H36,O33,H46,C34,O35,N36,H48,C37,H37,H38,C38,H39,H4A,C39,O40,N41,H41,C42,H42,H43,C43,H44,H45,S44,H47

  • 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

  • SEC: Serine with reduced vdw on the OG oxygen for covalent docking
    Atoms:
    N,HN,CA,HA,CB,HB1,HB2,OG,C,O

  • 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