1
???????????? ?????? ???????? ??????????????????

• ??????????? ?????? ??????????????
  ?????????????????? ?????, ????????????
  ??????????????? ????? ???????? ??????
  ???????????.
• ??? ????? ??????
• ?????????? ??????-?????????? ?????????? ?????
• ???????????? ????????? ??????????? ??????????
• ???????????, ???????????? ??????? ????????,
  ??????????????? ????????
• ????-?????????????? ???????????
• ?????????????? ??????, ?????????????? ?
  ?????????????? ??????????

2
???????????? ?????? ???????? ??????????????????

• ? ??? ??? ????? ??????
• The ExPASy server ??????????
  http//www.expasy.ch/tools/primary
• The Swiss EMBnet coiled-coil ???????,
  ???????????? ? ??. ??????. ??????
• http//www.ch.embnet.org
• The CBS Prediction Servers ???????????,
• ????-?????????????? ???????????
• http//www.cbs.dtu.dk/services

3
????????? ??? ???????????? ??????-??????????
?????????? ????? ProtParam
4
ProtParam
5
ProtParam

• Molecular weight (?? ????????? ????-??????????????
  ???????????)
• ?????????????? ??????
• ????????????? pI
• Extinction coefficients (280 nm) (?? ?????????
  ???????????????? ?????????????? ???????????)
• Instability (????? 40 ??????) ??????????????
  ? ???????????? (test tube, ?????????? ??????????)
• Half-life (yeast in vivo, mammalian reticulocytes
  in vitro, Escherichia coli in vivo N-terminal
  rule)
• ????????????? ??????
• Grand average of hydropathicity (GRAVY)
  ?????????????? (-), ????????????? ()

6
Compute pI/Mw
?????????? ??????? ????? (??? ???? ?????), ???
???? ??????????? ????????????? pI ? ????????????
???
7
?????????? ????????? ?? ?????????? ??????????
PeptideMass
????? ????????? ??? ?? ?????????
????-?????????????? ??????????? ??? ?????? ??
Swiss-Prot, ? ????? ????????????, AS ???????? ?
?????????
8
PeptideMass - output
9
PeptideCutter
??? ???????? ? ???????????? ????? ??????? ??????
??????, ? ??????? ????? ????????? ???????????
??????????? ?? ??????? ???????
10
PeptideCutter - output
11
PeptideCutter - output
12
????? ??????????? ????

• ????????????? ?????????????????? ? ?????????
  ???????????, ???????? ??????????? ?? ????.
  ???????? ????????????? ??????? ????????????.
  Output ??????
• Seq. LQAPVLPSDLLSWSCVGAVGILALVSFTCV
• lt------gt Window 1
• lt------gt Window 2
• lt------gt Window 3
• ?????? ???? ?????? ??????????????? ????????????
  ??????? ?????????????? ???????? (??? ?? 19!)

• ??????, ?????????? ?? ??????? ??????????? ????,
  ??? ???????, ?? ?????????????? ??????????. ???
  ????????????? ?????
• ????????? ?????? ????? ????? ?????????? ???????
• ?? ????????? ?? ?????????? ????????? ???????
  ????, ??????????? ?????? ? ?.?.

13
???????????? ??????????????? ????????? ProtScale
56 ?????????????? ???? (? ?????????????
????????), ?????????? ???? -gt ????? ?????? ????
14
ProtScale - output
?????????? ????? ??? ?????? 1.6. ????? ???????
?? ???
15
????? ??????? ???????????? ???????????????
????????? TMHMM
Transmembrane beta barrel prediction PROFtmb
(http//rostlab.org/services/proftmb )
PRED-TMBB (http//biophysics.biol.uoa.gr/PRED-TMB
B/) TBBPred (http//www.imtech.res.in/raghava/tb
bpred )
16
TMHMM - ??????????
??????? ?????? 7! TMs
TMHMM ????????????? ????????, ? ????? ?????????
????????????? ????????
17
??????

• ????? ??????????? ??????????? ??????? ? ?????.
  ????? ????????????? ????? ?????, ??????????
  ??????????? (???? ????????, ????????). ???
  ???????, ?????? ????? ?????? ???? ???? ? ???????
  ????? (????????? ??? ??? ???, ???????? ????????
  ???? ? ?.?.)
• ?????? ????????? ????? ????????? ??????? ????
  ??????? ????????????????, ????????? ??????? ???
  ??????? ????? ???????????? ??????
• ????? ?????? ????? ?????????? ????? ? ??? ???????
  gt ?????????? ????? ???????? ? ????????? ????????
  ?????????. ????? ????????

18
??????? ????????? ???????

• 1980?? PROSITE ?????? ??????? ????????? ?
  ??????, ???????????? ???????
• 1987 ???????? ??????? (Gribskov)
• position specific scoring schema ???
  ??????????? ??? ?????? ???????????? ?????????? ?
  ?????? ??????? ??????
• ?????? 1990? BLOCKs, PRINTs, Prodom
• PfamA ????????? ?????????, ????????????
  ??????? (?????? ????? ?????????? HMM)

19
3 ??????? ??? ?????? ???????

• InterProScan
• http//www.ebi.ac.uk/InterProScan
• CD (Conserved Domain) server (NCBI)
• http//www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cg
  i
• Pfscan
• http//hits.isb-sib.ch/cgi-bin/PFSCAN

20
InterPro

• InterPro is a database of protein families,
  domains and functional sites in which
  identifiable features found in known proteins can
  be applied to unknown protein sequences.
• ????????????? ?????????? ?? ?????????
  ?????????????? ?????? ???? ??? ??????
  ?????????????? ??????? ? ????????, ?????????? ???
  ????????? ??????????
• ? 2001 ???? Release 18.0 75.6 UniProt

21
??? ??? ??????????

• ?????? InterPro ????????? ?????????? ?????????
  ????????? ?????? ??? ??????, ??????????? ???? ?
  ??? ?? ????? ???????? ??? ?????, ?????????????
  ???? ?? ????? ?? ????????? ???. ???????????? IP
  ????????? ???????? ????????? ??????? ? ?????????
  ??????????????? ???????? ???????.

22
????? ??????? InterProScan
23
InterProScan - ??????????
24
Table View
25
CD server
Input - Accession number, gi ???
?????????????????? ? FASTA ???????
26
CD server output
??????? SMART, ????? Pfam, ???????
COGs ?????? ????? ????????? ?? ????????
??????!!!! ?????? ? ??????????? ????? ???????
???????? ??????? ??????
27
CDART ????? ?????? ? ??????????? ????????
??????????
28
Pfscan
??? ???????, ???????? ????????? ?????
29
Pfscan - output
30
??????????? ?????? Pfscan

• ????? ???????, ??? ?????? ??? ????????
• ?? ???????? ??????? ??????? ? ????????????
  ???????
• ????? ??????????? ??????? ???? ? ???????
  ??????????? ? ??? !
• ????? ??????? ??????????? ????? ??? ??????? ????
  ? scores (??????? score ??????? ???)

31
Match detail (??? ??????????? ?????)