From owner-chemistry@ccl.net Sat Jan 17 01:21:01 2009 From: "hirdesh kumar hirdeshs8*gmail.com" To: CCL Subject: CCL: Induced Fit docking: Schrodinger Message-Id: <-38452-090117011654-11001-VD81zq2LFIA44QWR7zTSdw^^^server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=0016e652fe7e1f886a0460a7a2ee Date: Sat, 17 Jan 2009 11:46:41 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8[A]gmail.com] --0016e652fe7e1f886a0460a7a2ee Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All; I am troubling with Induced fit docking module of schrodinger. Is there anyone familiar with this module -- Hirdesh Kumar Sharma M.S. 4th Semester A-212; Educational Block Center for Pharmacoinformatics NIPER, Sector 67, S.A.S. Nagar, Mohali Punjab-160062 --0016e652fe7e1f886a0460a7a2ee Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All;
I am troubling with Induced fit docking module of schrodinger. Is there anyone familiar with this module

--
Hirdesh Kumar Sharma
M.S. 4th Semester
A-212; Educational Block
Center for Pharmacoinformatics
NIPER,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062
--0016e652fe7e1f886a0460a7a2ee-- From owner-chemistry@ccl.net Sat Jan 17 12:56:01 2009 From: "Michel Petitjean petitjean.chiral{=}gmail.com" To: CCL Subject: CCL: clustering docked poses Message-Id: <-38453-090117043745-29836-jhJc+tC82OEBIUhHGhY2iQ|*|server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=000e0cd402dc2ce4480460aa703f Date: Sat, 17 Jan 2009 10:37:28 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral**gmail.com] --000e0cd402dc2ce4480460aa703f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit *There is some ambiguity about which set is to be translated and rotated. I did not mean that the ligand is moved and the enzyme is fixed. If so, a rigid ligand would be perfectly superposed to any translated and rotated copy of itself. I meant that the whole complex ligand-enzyme, when compared to an other complex of the same ligand and the same enzyme, needs that the RMSD is computed in a common set of cartesian coordinates. This is not ensured, in general. So, either the enzyme is superposed to itself (the minimized RMSD is not null if the enzyme structure changes, even slightly), or, the full complexes are superposed (the minimized RMSD is not null unless the complexes are identical). About the pairwise correspondence: this latter is read as an input data by ARMS, but it is computed as an output result by CSR (returns also the maximal common 3D motif). Other debate: I do not encourage the use of Excel, Word, etc. which use non standard binary formats not suitable for professional uses such as reading files by our own programmes (say, in f77, or in C,..), converting formats, exporting data to other applications, etc. All the best, **Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean]-[cea.fr, petitjean.chiral]-[gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html ....................................................................................................... * Sent to CCL by: maxim totrov [max*o*molsoft.com] For docking poses (as opposed to conformational analysis), you usually do not want to minimize RMSD for rotations and translations (RMSD with superposition). As an extreme case, consider completely rigid ligand: you still might have many distinct docked poses, but RMSD with superposition will always be zero. On the other hand, an important issue arises if there are symmetric moieties in your molecules - one has to consider different possible correspondences between equivalent atoms in two poses. Think of a flipping phenyl moiety for example. Excel will not detect that. Among other software, Molsoft's free Browser can calculate either static or superimposed RMSDs, with or without consideration of symmetries. Scripting language allows easy batch processing. Best regards, Max Totrov Sent to CCL by: "PETITJEAN Michel" [michel.petitjean:cea.fr] Does Excel minimizes the RMSD for all rotations and translations ? If not, you need a software such as ARMS or CSR. Michel Petitjean DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean^^cea.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html --000e0cd402dc2ce4480460aa703f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable There is some ambiguity about which set is to be translated and rotated= .
I did not mean that the ligand is moved and the enzyme is fixed.
If= so, a rigid ligand would be perfectly superposed to any translated
and = rotated copy of itself.
I meant that the whole complex ligand-enzyme, when compared  to
an= other complex of the same ligand and the same enzyme,
needs that the RM= SD is computed in a common set of cartesian
coordinates. This is not ens= ured, in general.
So, either the enzyme is superposed to itself (the minimized RMSD
is not= null if the enzyme structure changes, even slightly), or,
the full comp= lexes are superposed (the minimized RMSD is not null
unless the complexe= s are identical).
About the pairwise correspondence: this latter is read as an input data
= by ARMS, but it is computed as an output result by CSR (returns also
the= maximal common 3D motif).
Other debate: I do not encourage the use of E= xcel, Word, etc.
which use non standard binary formats not suitable for professional
uses= such as reading files by our own programmes (say, in f77, or in C,..),
= converting formats, exporting data to other applications, etc.

All t= he best,

Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA S= aclay, bat. 528,
91191 Gif-sur-Yvette Cedex, France.
Phone: +331 6908= 4006 / Fax: +331 6908 4007
E-mail: michel.petitjean]-[cea.fr, petitjean.chiral]-[gmail.com
http= ://petitjeanmichel.free.fr/itoweb.petitjean.shape.html
.............= ...........................................................................= ...............
 Sent to CCL by: maxim totrov [max*o*molsoft.com]
For docking poses (as oppose= d to conformational analysis), you usually do not want to minimize RMSD for rotations and translations (RMSD= with superposition). As an extreme case, consider completely rigid lig= and: you still might have many distinct docked poses, but RMSD with superposition will always be zero.
On the other hand, an importan= t issue arises if there are symmetric moieties in your molecules - one has to consider different possi= ble correspondences between equivalent atoms in two poses. Think of a flipping phenyl moiety for example. Excel will not detect that. Among other software, Molsoft's free Browser can calculate ei= ther static or superimposed RMSDs, with or without consideration of symmetries. Scripting language allows easy batch processing. 
 Best regards,
 Max Totrov
<= blockquote style=3D"border-left: 0.2em solid rgb(85, 85, 238); margin: 0em;= padding-left: 0.85em;">
 Sent to CCL by: "=
PETITJEAN Michel" [michel.petitjean:cea.fr]

 Does Excel minimizes the RMSD for all rotations and translations ?
 If =
not, you need a software such as ARMS or CSR.
 Michel Petitjean
 DSV/=
iBiTec-S/SB2SM (CNRS URA 2096)
 CEA Saclay, bat. 528
 91191 Gif-sur-Y=
vette Cedex, France.

 Phone: +331 6908 4006 / Fax: +331 6908 4007
 E-mail: michel.petitjean^^=
cea.fr
 http://petitjeanm=
ichel.free.fr/itoweb.petitjean.freeware.html
=20 =20 =20 --000e0cd402dc2ce4480460aa703f--