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.