The structure of a prote
in determ
ines
its b
iolog
ical funct
ion(s) and
its
interact
ions w
ith other factors; the b
ind
ing reg
ions tend to be conserved
in sequence and structure, and the
interact
ing res
idues
involved are usually
in close 3D space. The Prote
in Data Bank currently conta
ins more than 110 000 prote
in structures, approx
imately one-th
ird of wh
ich conta
in metal
ions. Ident
ify
ing and character
iz
ing metal
ion-b
ind
ing s
ites
is thus essent
ial for
invest
igat
ing a prote
in’s funct
ion(s) and
interact
ions. However, exper
imental approaches are t
ime-consum
ing and costly. The web server reported here was bu
ilt to pred
ict metal
ion-b
ind
ing res
idues and to generate the pred
icted metal
ion-bound 3D structure. B
ind
ing templates have been constructed for reg
ions that b
ind 12 types of metal
ion-b
ind
ing res
idues have been used to construct b
ind
ing templates. The templates
include res
idues w
ith
in 3.5 Å of the metal
ion, and the fragment transformat
ion method was used for structural compar
ison between query prote
ins and templates w
ithout any data tra
in
ing. Through the adjustment of scor
ing funct
ions, wh
ich are based on the s
im
ilar
ity of structure and b
ind
ing res
idues. Twelve k
inds of metal
ions (Ca
2+, Cu
2+, Fe
3+, Mg
2+, Mn
2+, Zn
2+, Cd
2+, Fe
2+, N
i2+, Hg
2+, Co
2+, and Cu
+) b
ind
ing res
idues pred
ict
ion are supported. MIB also prov
ides the metal
ions dock
ing after pred
ict
ion. The MIB server
is ava
ilable at
ioinfo.cmu.edu.tw/MIB/" class="extLink">http://bioinfo.cmu.edu.tw/MIB/.