From owner-chemistry@ccl.net Sun Jul 13 14:39:00 2008 From: "RICHARD JILL WOOD rwoodphd!A!msn.com" To: CCL Subject: CCL: Protein-Ligand CONSTRAINED Docking Message-Id: <-37338-080711084506-22134-NZ4N15fAzz7dxx17EBNK2Q!=!server.ccl.net> X-Original-From: RICHARD JILL WOOD Content-Type: multipart/alternative; boundary="_fbdd8ff9-897e-4ffb-82fe-1153fddfdfaf_" Date: Fri, 11 Jul 2008 12:12:09 +0000 MIME-Version: 1.0 Sent to CCL by: RICHARD JILL WOOD [rwoodphd^msn.com] --_fbdd8ff9-897e-4ffb-82fe-1153fddfdfaf_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Vidana=2C I assume that -fmatch is command-line. If not=2C I am not sure how it work= s. Believe me=2C I've explored Surflex-Dock very extensively these past fe= w days (including reading the manual!) and it just doesn't do what I would = like it to do. We've had several bad experiences with Glide=2C including its inability to = recreate the "docking poses" of ligands bound to proteins as found in sever= al known crystal structures. Richard > From: owner-chemistry^^^ccl.net > To: rwoodphd^^^msn.com > Subject: CCL: Protein-Ligand CONSTRAINED Docking > Date: Fri=2C 11 Jul 2008 14:23:51 +1000 >=20 >=20 > Sent to CCL by: [Vidana.Epa^csiro.au] >=20 > Hi Richard=2C >=20 > Doesn't the "-fmatch" option of Surflex-Dock (constraining the > docking to a pre-placed fragment) do what you need to achieve? >=20 > I am also curious as to why you came to the conclusion that > Glide is not up to your standards. >=20 >=20 > Cheers=2C >=20 > Vidana. >=20 >=20 >=20 > Vidana C. Epa > =20 > CSIRO=2C > Division of Molecular Health & Technologies=2C > 343 Royal Parade=2C > Parkville=2C Victoria 3052=2C > AUSTRALIA. > =20 > tel: (61) - 3 - 9662 - 7345 > fax:(61) - 3 - 9662 - 7347 > =20 > email: Vidana.Epa(!)csiro.au > -----Original Message----- > > From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net]=20 > Sent: Friday=2C 11 July 2008 8:07 AM > To: Epa=2C Vidana (CMHT=2C Parkville) > Subject: CCL: Protein-Ligand CONSTRAINED Docking >=20 >=20 > Sent to CCL by: "Richard Wood" [rwoodphd##msn.com] > Hi all=2C >=20 > I have a series of ligands which I've docked to a protein using=20 > Surflex-Dock as implemented in Sybyl. >=20 > Unfortunately=2C my results don't explain some experimental observations= =20 > so I would like to do some contrained docking. >=20 > I've been looking into FlexX-Pharm=2C but it seems to only allow one to > constrain an ELEMENT of the ligand to be a certain radius from a > certain atom (which one can choose) in the protein target. For > example=2C one can pick a nitrogen in a ligand to be within a 3.0 > Angstrom radius of a given protein atom=2C say. >=20 > This is problematic if your ligand has several nitrogens or carbons in=20 > them=2C as one cannot pick atom types or atom numbers. I'm wondering if= =20 > there is a workaround to this=3B I'd like to stay with Sybyl as my boss=20 > wants me to use it=2C and we've decided Glide is not up to our standards.= =20 >=20 > To conclude=2C I would like to be able to pick a particular ligand atom > and > constrain it to be a certain distance from a protein atom=2C that I again > pick=2C and then dock it. As it stands now=2C I can only constrain a (an= y) > nitrogen in my ligand (I think the fact that my ligand is not > introduced at any point=2C prior to docking=2C into this process is what = is > problematic) to be within a radius of a protein atom=2C and not a fixed > distance. >=20 > Basically=2C I want to constrain an imidazole nitrogen > (say) to be 2.4 Angstroms away from an iron atom in a heme group=2C or a > methyl group to be 3.0 Angstroms from the same atom=2C and not WITHIN a > radius of this distance=2C since it can be anywhere from 0 to the > distance I want=2C and lead to situations I'm seeing now=2C where the > molecule I'm docking is on top of the heme. >=20 > TIA=2C > Richard >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageJ= ob: http://www.ccl.net/jobs>=20 >=20 > -=3Dis is automatically added to each message by the mailing script =3D > To recover the email address of the author of the message=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20 > Search Messages: http://www.ccl.net/htdig (login: ccl=2C Password: searc= h) >=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 _________________________________________________________________ It=92s a talkathon =96 but it=92s not just talk. http://www.imtalkathon.com/?source=3DEML_WLH_Talkathon_JustTalk= --_fbdd8ff9-897e-4ffb-82fe-1153fddfdfaf_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi Vidana=2C

I assume that -fmatch is command-line. =3B If not= =2C I am not sure how it works. =3B Believe me=2C I've explored Surflex= -Dock very extensively these past few days (including reading the manual!) = and it just doesn't do what I would like it to do.

We've had several= bad experiences with Glide=2C including its inability to recreate the "doc= king poses" of ligands bound to proteins as found in several known crystal = structures.

Richard

>=3B From: owner-chemistry^^^ccl.net
&= gt=3B To: rwoodphd^^^msn.com
>=3B Subject: CCL: Protein-Ligand CONSTRAIN= ED Docking
>=3B Date: Fri=2C 11 Jul 2008 14:23:51 +1000
>=3B
= >=3B
>=3B Sent to CCL by: [Vidana.Epa^csiro.au]
>=3B
>= =3B Hi Richard=2C
>=3B
>=3B Doesn't the "-fmatch" option of Sur= flex-Dock (constraining the
>=3B docking to a pre-placed fragment) do = what you need to achieve?
>=3B
>=3B I am also curious as to why= you came to the conclusion that
>=3B Glide is not up to your standard= s.
>=3B
>=3B
>=3B Cheers=2C
>=3B
>=3B Vidana.>=3B
>=3B
>=3B
>=3B Vidana C. Epa
>=3B
>= =3B CSIRO=2C
>=3B Division of Molecular Health &=3B Technologies=2C=
>=3B 343 Royal Parade=2C
>=3B Parkville=2C Victoria 3052=2C
&= gt=3B AUSTRALIA.
>=3B
>=3B tel: (61) - 3 - 9662 - 7345
>= =3B fax:(61) - 3 - 9662 - 7347
>=3B
>=3B email: Vidana.Epa(!)cs= iro.au
>=3B -----Original Message-----
>=3B >=3B From: owner-ch= emistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net]
>=3B Sent: Frida= y=2C 11 July 2008 8:07 AM
>=3B To: Epa=2C Vidana (CMHT=2C Parkville)>=3B Subject: CCL: Protein-Ligand CONSTRAINED Docking
>=3B
>= =3B
>=3B Sent to CCL by: "Richard Wood" [rwoodphd##msn.com]
>= =3B Hi all=2C
>=3B
>=3B I have a series of ligands which I've do= cked to a protein using
>=3B Surflex-Dock as implemented in Sybyl.>=3B
>=3B Unfortunately=2C my results don't explain some experimen= tal observations
>=3B so I would like to do some contrained docking.<= br>>=3B
>=3B I've been looking into FlexX-Pharm=2C but it seems to = only allow one to
>=3B constrain an ELEMENT of the ligand to be a cert= ain radius from a
>=3B certain atom (which one can choose) in the prot= ein target. For
>=3B example=2C one can pick a nitrogen in a ligand t= o be within a 3.0
>=3B Angstrom radius of a given protein atom=2C say.=
>=3B
>=3B This is problematic if your ligand has several nitrog= ens or carbons in
>=3B them=2C as one cannot pick atom types or atom = numbers. I'm wondering if
>=3B there is a workaround to this=3B I'd = like to stay with Sybyl as my boss
>=3B wants me to use it=2C and we'= ve decided Glide is not up to our standards.
>=3B
>=3B To concl= ude=2C I would like to be able to pick a particular ligand atom
>=3B a= nd
>=3B constrain it to be a certain distance from a protein atom=2C t= hat I again
>=3B pick=2C and then dock it. As it stands now=2C I can = only constrain a (any)
>=3B nitrogen in my ligand (I think the fact th= at my ligand is not
>=3B introduced at any point=2C prior to docking= =2C into this process is what is
>=3B problematic) to be within a radi= us of a protein atom=2C and not a fixed
>=3B distance.
>=3B
&= gt=3B Basically=2C I want to constrain an imidazole nitrogen
>=3B (say= ) to be 2.4 Angstroms away from an iron atom in a heme group=2C or a
>= =3B methyl group to be 3.0 Angstroms from the same atom=2C and not WITHIN a=
>=3B radius of this distance=2C since it can be anywhere from 0 to th= e
>=3B distance I want=2C and lead to situations I'm seeing now=2C whe= re the
>=3B molecule I'm docking is on top of the heme.
>=3B
= >=3B TIA=2C
>=3B Richard
>=3B
>=3B
>=3B
>=3B = -=3D This is automatically added to each message by the mailing script =3D-=Job: = http://www.ccl.net/jobs
>=3B
>= =3B
>=3B -=3Dis is automatically added to each message by the mailing= script =3D
>=3B To recover the email address of the author of the mes= sage=2C please change
>=3B the strange characters on the top line to t= he ^^^ sign. You can also
>=3B look up the X-Original-From: line in the = mail header.
>=3B
>=3B E-mail to subscribers: CHEMISTRY^^^ccl.net = or use:
>=3B
= >=3B
>=3B E-mail to administrators: CHEMISTRY-REQUEST^^^ccl.net or us= e
>=3B
>=3B=
>=3B
>=3B http://www.ccl.net/chem= istry/sub_unsub.shtml
>=3B
>=3B Before posting=2C check wait tim= e at: http://www.ccl.net
>=3B
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>=3B
>=3B

It=92s a talkathon =96 but i= t=92s not just talk. Check out the i=92m Talkathon. = --_fbdd8ff9-897e-4ffb-82fe-1153fddfdfaf_--