back>[[PDB toolbox]]&br;&br;
*decoy ligand½Å¿´¤ÎʬÉÛ¿Þ¤òºî¤ë [#qfd51db7]
''Ìܼ¡''
#contents
**³µÍ× [#l2011d96]
¥¿¥ó¥Ñ¥¯¼Á¥É¥Ã¥¥ó¥°¤Çºî¤Ã¤¿¥ê¥¬¥ó¥É¤ÎʬÉÛ¿Þ¤òºî¤ê¤Þ¤¹¡¥&br;
¤³¤ó¤Ê´¶¤¸¤Î³¨¤òÉÁ¤¯¤Î¤¬ÌÜɸ¤Ç¤¹¡¥&br;
#ref(1ACB_Centers.png)
¿¿¤óÃæ¤Î¥¿¥ó¥Ñ¥¯¼Á(receptor)¤Î¼þ¤ê¤Î¥ê¥¬¥ó¥É¥¿¥ó¥Ñ¥¯¼Á¤Îͽ¬°ÌÃÖ¤ò½Å¿´¤Î¤ß¤Ç¼þ¤ê¤Ëɽ¼¨¤·¤Æ¤¤¤Þ¤¹¡¥&br;
ÀÖ¤¤ÅÀ¤Ï³Æ¸õÊ乽¤¡¤²«¿§¤¤µå¤Ï¾å°Ì1¡Á10°Ì¤Î¸õÊ乽¤¡¤¥Ô¥ó¥¯¤Î¥ê¥Ü¥ó¤ÏÀµ²ò°ÌÃ֤Υꥬ¥ó¥É¥¿¥ó¥Ñ¥¯¼Á¤Ç¤¹¡¥&br;
¥É¥Ã¥¥ó¥°¥Ä¡¼¥ë¤ÏMEGADOCK¤ª¤è¤ÓZDOCK¤òÁÛÄꤷ¤Æ¤¤¤Þ¤¹¡¥&br;
»È¤¦¥Ä¡¼¥ë¤Ï°ìÈÖ²¼¤Ë¤Þ¤È¤á¤Þ¤·¤¿¡¥> [[¥Ä¡¼¥ë·²>http://www.bi.cs.titech.ac.jp/~ohue/index.php?decoy%20ligand%BD%C5%BF%B4%A4%CE%CA%AC%C9%DB%BF%DE%A4%F2%BA%EE%A4%EB#a4a7ab47]]
**Ligand (decoy) PDB¤òºî¤ë [#e90db7f6]
¥É¥Ã¥¥ó¥°¤µ¤»¤¿Ligand¤ÎPDB¤òºî¤ê¤Þ¤¹¡¥&br;
MEGADOCK¤äZDOCK¤Ç¤Ï¥É¥Ã¥¥ó¥°¤µ¤»¤¿Ê£¹çÂι½Â¤¤Ï¡¤
out¥Õ¥¡¥¤¥ë¤ÎÃæ¤Ë²óž³Ñ¾ðÊó¤ÈºÂɸ¾ðÊó¤Î¤ßµºÜ¤µ¤ì¤Æ¤¤¤Þ¤¹¡¥
¤³¤³¤«¤éPDB¥Õ¥¡¥¤¥ë¤òÀ¸À®¤·¤Þ¤¹¡¥
´ðËÜŪ¤Ë¤ÏMEGADOCK¤Îdecoygen¡¤ZDOCK¤Îcreate.pl/create_lig¤ò»È¤¤¤Þ¤¹¡¥&br;
2000¸Ä¤Î¸õÊ乽¤¤òÀ¸À®(MEGADOCK/ZDOCK¤Î¥Ç¥Õ¥©¥ë¥È)¤·¤¿¤È¤·¤Æº£¸å¤ÎÀâÌÀ¤ò¹Ô¤¤¤Þ¤¹¡¥
-MEGADOCK (zshɽµ)
for i (`seq 1 2000`) ./decoygen decoy.$i.pdb ligand.pdb docking.out $i
-ZDOCK
create.pl docking.out¡¡¡Ê.out¥Õ¥¡¥¤¥ë¤ËµºÜ¤Î¥Ñ¥¹¤ÎPDB¤ò»²¾È¤·¤Þ¤¹¡Ë
ZDOCK¤Î¾ì¹ç¡¤3.0.2¤È¤½¤ì°ÊÁ°¤Î¥Ð¡¼¥¸¥ç¥ó¤È¤Ç¤Ï·Á¼°¤¬ÊѤï¤Ã¤Æ¤¤¤Þ¤¹¤Î¤ÇÃí°Õ¤¬É¬ÍפǤ¹¡¥&br;
¤½¤Î¾¤Î¥É¥Ã¥¥ó¥°¥Ä¡¼¥ë¤Ç¤â¡¤¥ì¥»¥×¥¿¡¼¤Î°ÌÃÖ¤¬ÊѲ½¤»¤º¥ê¥¬¥ó¥É¤Î¤ß¤ÎºÂɸ(PDB)¤Ç¸õÊä²ò¤¬µ½Ò¤µ¤ì¤Æ¤¤¤ì¤Ð¤³¤Î¸å¤Î½èÍý¤ÏƱÍͤǤ¹¡¥
**Ligand decoy¤Î½Å¿´ºÂɸ¤ò·×»»¤·¤Æ¥Õ¥¡¥¤¥ë¤Ë¤Þ¤È¤á¤ë [#v4f0c19b]
***½Å¿´ºÂɸ¤ò·×»»¤¹¤ë [#t8f61241]
2000¸Ä¤ÎPDB¤¬¤Ç¤¤Þ¤·¤¿¡¥¤³¤ì¤é¤Î½Å¿´ºÂɸ¤ò·×»»¤·¤Þ¤¹¡¥&br;
½Å¿´·×»»¤Ë¤Ï[[pdb-Tools>https://pdb-tools.googlecode.com/files/pdbTools_0.2.1.tar.gz]]¤ò»È¤¤¤Þ¤¹¡¥&br;
python¤¬¤¢¤ì¤Ð¥À¥¦¥ó¥í¡¼¥É¤·¤ÆŬÅö¤Ê¥Ç¥£¥ì¥¯¥È¥ê¤ËŸ³«¤·¤Æ»È¤¨¤Þ¤¹¡¥&br;
¥Û¡¼¥à¥Ç¥£¥ì¥¯¥È¥ê¤Î ~/src/¤ËŸ³«¤·¤¿¤È¤·¤ÆÏäò¿Ê¤á¤Þ¤¹¡¥
$ ~/src/pdbTools_0.2.1/pdb_centermass.py ligand.pdb
ligand.pdb 11.4160 9.2530 2.8806
¤È¤¤¤¦·Á¤Ç½ÐÎϤµ¤ì¤Þ¤¹¡Ê¥¹¥Ú¡¼¥¹¶èÀÚ¤ê¤Ç¤¹¡Ë¡¥&br;
¤½¤Î¤Þ¤Þ¤Ç¤ÏÈó¾ï¤Ë»È¤¤¤Å¤é¤¤¤Î¤Ç¡¤¥«¥ó¥Þ¶èÀÚ¤ê¤Îcsv¤Ë¤·¤Æ¤·¤Þ¤¤¤Þ¤·¤ç¤¦¡¥&br;
-cmcoord.sh
#!/bin/sh
cmtext=`~/src/pdbTools_0.2.1/pdb_centermass.py $1`
echo $cmtext | sed "s/ /, /g" | cut -d , -f 1,2,3,4
¤³¤ì¤Ç
$ bash cmcoord.sh ligand.pdb
ligand.pdb, 11.4160, 9.2530, 2.8806
¤È¤Ê¤ê¤Þ¤¹¡¥&br;
2000¸Ä¤Îdecoy¤Î½Å¿´ºÂɸ¤ò·×»»¤¹¤ë¤Ë¤Ï¡¤
$ for i (`seq 1 2000`) { bash cmcoord.sh decoy.$i.pdb; } > Centers.csv
¤È¤¹¤ë¤È¡¤Centers.csv¤Ëdecoy.1.pdb¤«¤édecoy.2000.pdb¤Þ¤Ç¤Î½Å¿´¤¬µÏ¿¤µ¤ì¤Þ¤¹¡¥
¤Ê¤ª¡¤pdbTools¤Îpdb_centermass.py¤Ï¥¨¥ì¥á¥ó¥ÈÎ󤬤Á¤ã¤ó¤È¤Ê¤¤¤ÈÆ°¤¤Þ¤»¤ó¡¥&br;
PDB¥Õ¥¡¥¤¥ë¤ÎÃæ¤Ë¤Ï¥¨¥ì¥á¥ó¥ÈÎ󤬥ƥ¥È¥¦¤Ë¤Ê¤Ã¤Æ¤¤¤ë¤Î¤â¿¤¤¤Î¤Ç¡¤
¤½¤Î¾ì¹ç¤Ï°Ê²¼¤Î¥¹¥¯¥ê¥×¥È¤ÇåºÎï¤Ë¤·¤Þ¤·¤ç¤¦¡¥¡ÊBiopython¤¬É¬ÍפǤ¹¡Ë
-pdbclean.py
#!/usr/bin/python
#
# Masahito Ohue
# python pdbclean.py pdbfile
import os
import sys
import Bio
from Bio.PDB import *
# delete terminal of rows
PDB = sys.argv[1]
fp = open(PDB, 'r')
line = fp.readlines()
fp.close()
fp = open(PDB, 'w')
for l in line:
fp.write(l[0:67]+"\n")
fp.close()
# add element columns by biopython
parser = PDBParser()
str = parser.get_structure("test1", PDB)
io = PDBIO()
io.set_structure(str)
io.save(sys.argv[1])
¤³¤ì¤Ç
$ python pdbclean.py ligand.pdb
¤È¤¹¤ë¤Èligand.pdb¤¬åºÎï¤Ë¤Ê¤Ã¤Æ¤¤¤Þ¤¹¡Ê¾å½ñ¤Ãí°Õ¡Ë¡¥&br;
decoy¤Îpdb¤òÀ¸À®¤¹¤ëÁ°¤Ë¤ä¤ê¤Þ¤·¤ç¤¦¡¥
***½Å¿´ºÂɸ¤ò¤Þ¤È¤á¤¿PDB¤òºî¤ë [#sf5b575d]
Centers.csv¤òÆɤ߼è¤Ã¤ÆPDB¥Ó¥å¡¼¥ï¤Çɽ¼¨¤Ç¤¤ë¤è¤¦¤Ë¤·¤Þ¤¹¡¥&br;
¶ñÂÎŪ¤Ë¤Ï½Å¿´ºÂɸ¤Ë¥Æ¥¥È¥¦¤Ê¸¶»Ò¡ÊFE¤È¤«¡Ë¤òÃÖ¤¤¤Æ¤ä¤ì¤ÐÎɤ¤¤Ç¤¹¡¥&br;
PDB¤Î·Á¼°¤ËÃí°Õ¤·¤Æ¥¹¥¯¥ê¥×¥È¤òÍÑ°Õ¤·¤Þ¤¹¡¥&br;
-pdbcm.py
#!/usr/bin/python
# Masahito Ohue
import os
import sys
import csv
cm = sys.argv[1]
line = csv.reader(open(cm))
i = 0
ch = "L" # chain name
for l in line:
i = i+1
xcoord = float(l[1])
ycoord = float(l[2])
zcoord = float(l[3])
print('HETATM %4d FE FE %s%4d %8.3f%8.3f%8.3f 1.00 1.00 C' % (i, ch, i, xcoord, ycoord, zcoord))
¤³¤ì¤Ç¡¤
$ python pdbcm.py Centers.csv > Centers.pdb
¤È¤¹¤ë¤È¡¤½Å¿´ºÂɸ¤òÅ´¸¶»Ò¤Ë¤·¤¿Centers.pdb¤¬¤Ç¤¤Þ¤¹¡¥&br;
receptor.pdb¤È¥Á¥§¥¤¥ó̾¤¬Èï¤é¤Ê¤¤¤è¤¦¤ËŬµ¹Êѹ¹¤·¤Æ²¼¤µ¤¤¡¥
**Centers.pdb¤òPyMOL¤Çɽ¼¨¤¹¤ë [#wa781be2]
¤¢¤È¤ÏCenters.pdb¤òPyMOL¤ËÆɤ߹þ¤Þ¤»¤ì¤ÐOK¤Ç¤¹¡¥&br;
¤·¤«¤·ÀßÄê¤ò¥Þ¥¦¥¹¤Ç¥«¥Á¥«¥ÁÊѤ¨¤ë¤Î¤âÌÌÅݤʤΤǡ¤¥¹¥¯¥ê¥×¥È¤ò½ñ¤¤¤Æɽ¼¨¤·¤Þ¤¹¡¥&br;
PyMOL¤Ïpython¥¹¥¯¥ê¥×¥È¤¬Æ°¤¯¤Î¤Ç¡¤¤½¤ì¤Ç¡¥&br;
¡Êpdbid¤ò°ú¿ô¤Ë¤·¤Æ¡¤¤¿¤È¤¨¤Ð1ACB_r_b.pdb¤È1ACB_Centers.pdb¤òɽ¼¨¤·¤Þ¤¹¡¥¡Ë
-decoys.py
def showdecoys(pdbid):
cmd.delete("all")
cmd.load(pdbid+"_r_b.pdb")
cmd.load(pdbid+"_Centers.pdb")
cmd.load(pdbid+"_l_b.pdb")
cmd.zoom("all")
cmd.hide("all")
cmd.bg_color("white")
cmd.set("ray_opaque_background", "0")
cmd.color("green", pdbid+"_r_b")
cmd.color("magenta", pdbid+"_l_b")
cmd.show("cartoon", "all")
cmd.select("lig", "chain L in "+pdbid+"_Centers.pdb")
cmd.hide("everything", "lig")
cmd.color("red", "lig")
cmd.set("sphere_scale", "0.15", "lig")
cmd.show("sphere", "lig")
cmd.select("top", "res 1-10 in chain L in "+pdbid+"_Centers.pdb")
cmd.set("sphere_scale", "0.7", "top")
cmd.show("sphere", "top")
cmd.color("yellow", "top")
cmd.ray()
cmd.png(pdbid+"_Centers")
¤³¤ì¤òPyMOL¤Î¥³¥Þ¥ó¥É¥¦¥£¥ó¥É¥¦¤Ç¡¤
PyMOL> run decoys.py
PyMOL> showdecoys("1ACB")
¤ÈÆþÎϤ¹¤ì¤Ð¡¤ºÇ½é¤Î¤è¤¦¤Ê¿Þ¤¬¤Ç¤¤Þ¤¹¡¥
**1ACB¤Ç¼ÂÎã [#wedb4bef]
ZLAB Protein-Protein Dockign Benchmark (http://zlab.umassmed.edu/benchmark/) ¤Î1ACB(bound)¤Ç¼ÂºÝ¤Ë¼Â¹Ô¤·¤Æ¤ß¤Þ¤¹¡¥&br;
1ACB_r_b.pdb¤È1ACB_l_b.pdb¤Ï¥¨¥ì¥á¥ó¥ÈÎ󤬤ʤ¤¤Î¤Ç¡¤ºÇ½é¤Ëpdbclean.pdb¤ò¤«¤±¤Æ¤¤¤Þ¤¹¡¥&br;
¥É¥Ã¥¥ó¥°¤Ë¤ÏMEGADOCK 4.0¤ò»È¤Ã¤Æ¤¤¤Þ¤¹¡¥&br;
''¡ PDB¤òåºÎï¤Ë¤·¤Æ¡¤MEGADOCK¡¤decoy¤ÎpdbÀ¸À®''
$ python pdbclean.py
$ ./megadock -R 1ACB_r_b.pdb -L 1ACB_l_b.pdb -o 1ACB_b.out
$ for i (`seq 1 2000`) ./decoygen 1ACB_l_b.$i.pdb 1ACB_l_b.pdb 1ACB_b.out $i
¡Ê1ACB_l_b.1.pdb¤«¤é1ACB_l_b.2000.pdb¤¬¤Ç¤¤Þ¤¹¡¥¡Ë
''¢ ½Å¿´ºÂɸ¤Î·×»»¡¤Å´¸¶»Ò¤ËÃÖ¤´¹¤¨¤¿PDB¤ÎÀ¸À®''
$ for i (`seq 1 2000`) { bash cmcoord.sh 1ACB_l.$i.pdb; } > 1ACB_Centers.csv
¡Ê¾¯¤·»þ´Ö¤¬¤«¤«¤ê¤Þ¤¹¡¥¤ªÃã¤Ç¤âÞ»¤ì¤Þ¤·¤ç¤¦¡¥¡Ë
$ python pdbcm.py 1ACB_Centers.csv > 1ACB_Centers.pdb
''£ PyMOL¤Ç¤Îɽ¼¨''&br;
PyMOL¤ò³«¤¤Þ¤¹¡¥¡Ê¥«¥ì¥ó¥È¥Ç¥£¥ì¥¯¥È¥ê¤Ë³ºÅö¤Îpdb¤¬¤¢¤ë¤â¤Î¤È¤·¤Þ¤¹¡¥¡Ë
PyMOL> run decoys.py
PyMOL> showdecoys("1ACB")
¤³¤ì¤Ç¥«¥ì¥ó¥È¥Ç¥£¥ì¥¯¥È¥ê¤Ëpng¥Õ¥¡¥¤¥ë¤¬¤Ç¤¤Þ¤·¤¿¤Í¡¥
#ref(1ACB_Centers.png)
**¥Õ¥¡¥¤¥ë¡¤´ØÏ¢¥Ä¡¼¥ë°ìÍ÷ [#a4a7ab47]
-MEGADOCK http://www.bi.cs.titech.ac.jp/megadock
-ZDOCK http://zdock.umassmed.edu/software/
-PDB-Tools https://code.google.com/p/pdb-tools/
-Biopython http://biopython.org
-¥¹¥¯¥ê¥×¥È [ [[¤Þ¤È¤á¤Æ¥À¥¦¥ó¥í¡¼¥É>http://www.bi.cs.titech.ac.jp/~ohue/script/centermass.zip]] ]
¤â¤·¤¯¤Ï
wget http://www.bi.cs.titech.ac.jp/~ohue/script/centermass.zip
--cmcoord.sh
--pdbclean.py
--pdbcm.py
--decoys.py