CCL: Docking programs
- From: "Forlani Roberto"
- Subject: CCL: Docking programs
- Date: Fri, 23 Feb 2007 16:40:30 +0100
Sent to CCL by: "Forlani Roberto"
> -----Original Message-----
> From: owner-chemistryccl.net [mailto:owner-chemistryccl.net]
> Sent: Friday, February 23, 2007 12:50 AM
> To: Forlani Roberto
> Subject: CCL: Docking programs
> Sent to CCL by: "Ronald L Cook" [cookrl###tda.com]
> Dear CCLers
> Many of the docking programs available calculate a fit
> between a host (e.g. an enzyme, etc) and a small molecule to
> look for small molecule drugs. My interest/need lies in the
> opposite direction. Does anyone know of a program that takes
> a guest and (using for example a genetic algorithm or other
> equivalent stochastic optimization method) builds a small
> peptide (or other molecular backbone) chain that provides a
> good fit to the small molecule?
> Ronald Cook
> Principal Scientist
> TDA Research, Inc.
I think you should give a look at the following publication:
ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands
Wei Chen and Michael K. Gilson*
Center for Advanced Research in Biotechnology, University of Maryland
Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850
Received June 12, 2006
Low-molecular-weight receptors that bind targeted guest molecules have a wide
range of potential applications but are difficult to design. This paper
describes an evolutionary method for computer-aided design of such receptors
that works by linking together chemical components from a user-defined library
around a stable conformation of the targeted ligand. The software can operate in
three modes: de novo design, in which it builds a wide variety of receptors from
small components; macrocycle design, in which it builds homopolymeric
macrocycles around the ligand; and elaboration of an existing receptor
structure. The top candidates generated by the automatic construction process
are further studied with detailed affinity calculations whose validity is
supported by prior studies of experimentally characterized host-guest systems.
All three modes of operation are illustrated here through the design of novel