Subject: Summary: conformational search

From: [email-masked] (Chris Chen)
Date: Mon, 2 May 94 09:30:42 -0700

Dear Netter:
Here comes the summray to my question about conformational
search . Thanks everyone for the help.
Chris Chen

----------------------- Original Question ----------------------------- 
>From [email-masked]  Thu Apr 21 01:31:48 1994
Subject: sysmatic conf. search and MC conf. search

Dear netters:

Can someone recommand  me some papers which evulate different 
conformational search methods, namely systematic conformational search 
and Monta Carlo conformational search?

Thanks in advance

Chris Chen
[email-masked] 
San Diego
	-- the finest city in the States
	
----------------------- Summary of Answers ----------------------------- 
From: [email-masked] (Wolf-D. Ihlenfeldt)

I think there was some review by Willet et al., J.Chem.Inf.Comput.Sci,
1994, 34

WDI
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From: [email-masked]

I have seen a very recent paper on complete 
conformational searching in MM-calculations 
compared with other methods. In its introduction 
it discusses a lot of other techniques (like MC, 
MD, grid search) and gives references for them.
I think it might be useful for you.
The reference is:

F. Villamagna and M. A. Whitehead
J. Chem. Soc. Faraday Trans., 90(1), 1994, pp. 47-54

Marcel Langoor.
Ing. M.H. Langoor
Analytical Molecular Spectrometry
Utrecht University
P.O. Box 80083
3508 TB Utrecht
The Netherlands
tel. +31 - 30 - 536811
fax  +31 - 30 - 518219
email: [email-masked]

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From: [email-masked] (Roberto Maiani)

About your problems you can see:
 JACS 1990 (112) 1419-1427 
 Macromolecules 1984 (17) 2044-2050

You can see also some articles published on "Reviews on Computational Chemistry"  
								Roberto Maiani
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From: [email-masked] (Eiji Osawa)

        I cannot overlook your message, because this is my field. The
following paper (of my own) discusses
the point you are looking for:
        H. Goto and E. Osawa, J. Chem. Soc., Perkin Trans. 2, 1993,
187-198.
Our point is that Monte Carlo conformation search can be inefficient when
high energy conformers are inherently more populated than the low energy
ones, which is actually the case for n-alkanes. because systematic search
explodes quickly under the heavy increase in computer time, it must be
efficient in the point that it should have some means to direct the space
search always to low-energy region.
More details are in that paper. Good luck! Eiji Osawa

/*********************************************************
*  Eiji Osawa                                            *
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From: [email-masked] (Adi Treasurywala)

Chris,
	My group and I have spent the been involved in a systematic
	survey of the applicability of the different methods of
	conformational analysis of small molecules for several years
	now. We have published two papers on teh subject using a
	standard set of molecules that will be applied to all of the
	methods in J Compu Chem. More work has of course been completed
	and I would be happy to discuss it with you on the phone if you
	are interested.

	If you get other responses please let me know. I would be
	interested in making sure that I have an up-to-date collection
	of references of others' work in this area.

Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road,
PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX
(215)983-5559, INTERNET [email-masked]

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From: [email-masked] (Craig W. Burkhart)

Almost any paper on rotational isomeric state (RIS) analyses by Paul
Flory and his coworkers would fit the bill. They were pioneers in
this form of work...

Craig W. Burkhart, Ph.D.                   Senior Research Chemist 
E-mail: [email-masked]             The Goodyear Tire & Rubber Co.
Fone:   216.796.3163                       Research Center
Fax:    216.796.3304                       142 Goodyear Boulevard
					   Akron, OH   44305
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From: Lipkowitz <[email-masked]>

Chris, I had that same question several years ago...along with many
others...so, Don Boyd and I started a review series to answer such questions. 
The answer to your question is: Andrew Leach, "A Survey of Methods for
Searching the Conformational Space of Small and Medium Sized Molecules" in
Reviews in Computational Chemistry, Volume 2, VCH Publishers, 1991.  Also see:
H.A. Scheraga, "Predicting Three-Dimensional Structures of Oligopeptides" in
Volume 3 of that series.  Both are complete tutorials that will help you.
Kenny.
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From: "Gregory L. Durst - DowElanco R&D" <[email-masked]>

The 2 *reviews* I'm aware of on conformational search are:
A. Howard & P. Kollman,  J. Med. Chem., v31,(9), (1988), 1669.
A. Leach in "Reviews in Computational Chemistry Vol.2" eds Boyd & Lipkowitz, 
 VCH Inc., NY, (1991), pp1-55.

Other papers on conformational searching possibly of interest:

M. Saunders, JACS, 109, (1987), 3150.
D. Ferguson & D. Raber, JACS, 111, (1989), 4371.
G. Chang, W. Guida & C. Still, JACS, 111, (1989), 4379 
T. Perkins & D. Barlow, J. Mol. Graphics, 8, (1990), 156.
M. Saunders et al, JACS, 112, (1990), 1419.

Hope this leads you to where you want to go!
Greg
+-----------------------------------------------------------------------+
|   Gregory L. Durst                   Computational Chemistry          |
|   phone:   317/337-3413              DowElanco  R&D                   |
|   email:   [email-masked]      9330 Zionsville Rd.  Bldg 306/D2 |
|                                      Indianapolis, IN  46268   USA    |
+-----------------------------------------------------------------------+
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From: R.G.A. Bone <[email-masked]>

J. Med. Chem., 31, 1831, (1988)
Chapter 1 of 'Reviews in Computational Chemistry, II', Ed. Lipkowitz and Boyd.
RGAB

R. G. A. Bone.
Molecular Research Institute,
845 Page Mill Road,
Palo Alto,
CA 94304-1011,
U.S.A.
Tel. +1 (415) 424 9924 x110
FAX  +1 (415) 424 9501
E-mail  [email-masked]

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From: Thomas Weimar <[email-masked]>

hi chris,
i can only point out some papers wich deal with monte-carlo simulations
on oligosaccharides. have a look at " Peters, et al., Carbohydr. Res. 238, 49-73, 1993.
this paper compares monte carlo vs. systematic conf. search.

the same monte carlo approach is used in "Stuike-Prill & Meyer, Eur. J. Biochem., 194, 903
-919, 1991. but thei program (GEGOP) is also able to calculate peptide or 
proteins.

hope that helps
thomas
---------------------------------------------------------
* Thomas Weimar (Ph. D.)    voice: 604 291 5650         *
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From: Max Vasquez <[email-masked]>
To: [email-masked]

Dear Chris,

       the "classical" test paper is by Saunders and co-workers; this appeared
in JACS 112, 1419-1427 (1990).  The authors compare several MC methods, MD,
DG, and systematic approaches to the conformational analysis of a cyclic
hydrocarbon.  You may also want to take a look at Goodman & Still in
J. Comp. Chem. 12, 110 (1991), Judson et al. J. Comp. Chem. 14, 1407 (1993),
and McGarrah et al J. Comp. Chem. 14, 1385 (1993).  The last two compare
systematic with "genetic algorithm" (GA) approaches.  There was another paper
in J. Comp. Chem. in 92 or so, I believe by a group in Germany or Switzerland,
which also addresses some of these issues -- I do not recall the reference for
that one.
========================================
Max Vasquez, PhD
Protein Design Labs, Inc.
2375 Garcia Ave.
Mountain View CA 94043
Phone (415) 903 3744   FAX (415) 903 3730
e-Mail  wk01189 @ worldlink.com
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