From adit@Kodak.COM  Tue Jul 20 12:20:26 1993
Date: Tue, 20 Jul 93 16:20:26 EDT
From: adit@Kodak.COM (Adi Treasurywala)
Message-Id: <9307202020.AA00501@bcc9.kodak.com>
To: chemistry@ccl.net
Subject: Summary of docking refs.


Folks,

	Sorry for the delay in summarizing for the net. Here is the
	table as I have it at present. Thanks to all for the help in
	getting it together. If anyone needs actual e-mail messages
	from which I extracted these refs I would be happy to send them
	out of course. The table is a bit wide. Sorry for the inconvenience.

Adi.

METHOD 		TRANS/ROT	SMALL FLEXIBILITY	MACRO FLEXIBILITY	REF
				TORS	ALL TERMS	TORS	ALL TERMS
BROWNIAN	
DYNAMICS
           	YES		NO	NO		NO	NO		2

SYSTEMATIC
SEARCH          NO              YES     NO              NO      NO              5

MONTE
CARLO
 macromodel	NO		YES	NO		NO	NO		1

ANNEALED
DYNAMICS
          	YES(?)		(?)	(?)		(?)	(?)		3

STERIC
FITTING
 DOCK		YES		NO	NO		NO	NO		4

MOLECULAR
DYNAMICS	YES(?)		YES	YES		YES	YES		8

MISCELLANEOUS
HYBRID METHODS  YES             YES     YES             NO      NO              6a
                NO              YES     YES(?)          NO      NO              6b,d,e
                YES             YES     YES             YES     YES             6c
                

DISTANCE 
GEOMETRY        YES             YES     YES(?)          NO      NO              7



REFERENCES:

1. W.C.Guida, R.S.Bohacek,M.D.Erion J.Compu.Chem. vol13, 214,(1992)
2.(a) S.A.Allison, S.H.Northrup, J.A.McCammon J.Chem.Phys., vol83 2894 (1985)
(b) S.H.Northrup, H.P.Erickson Proc.Nat'l.Acad.Sci. vol89, 3338 (1992)
3. Goodsell,D.S. & Olson, A.J. (1990) Automnated Docking of Substrates to Proteins
by Simulated Annealing.  Proteins vol. 8, 195-202.
4. I.D. Kuntz; Science vol 257, pg 1078-1082 (1992) and refs cited therein.
## Full MD simulations to determine the entire docking process of a ligand to a macromolecule 
   have not been reported to our knowledge. 
5. D.Meyer, C.B.Naylor, I.Motoc, G.R.Marshall, J.Comput-Aided Mol. Des. vol1, 3 (1987)
6a. C.M.Freeman, C.R.A.Catlow, J.M.Thomas, S.Brode,Chem. Phys.Lett., 186, 137-142 (1991)
6b. Moon, J. B.; Howe, W. J. Tetrahedron Comp. Method. 1990, 3, 697-711.
6c. Gallion, S. and Ringe, D. (1992) Protein Engng. 5, 291-300.
6d. A.R. Leach et al; J.Comput.Chem. vol 13, pg 730-748 (1992)
6e. S.H.Rotstein, M.A.Murcko J.Comput-Aided Mol. Des. vol7, 23 (1993)  
7. Blaney, J. M.; Dixon, J. S. Annual Reports in Medicinal Chemistry 1991, 26, 281-285. and references cited therein.
8.(a) B.L.Stoddard, D.E.Koshland Proc.Nat'l.Acad.Sci., vol90, 1146 (1993) and refs cited therein. (b) L.Banci, S.Schroder, P.A.Kollman, Proteins - Str. & Func. vol13, 288 (1992)

NB: This list is not meant to be exhaustive. It is merely intended to illustrate the different strategies that have been used to dock small molecules into larger ones with some key refs for each.