De novo programs

One class of Al-based computational chemistry programs are de novo programs. These programs generally try to efficiently automate tedious tasks by using some rational criteria to guide a trial-and-error process. For example. 

Table 10.4-4. Overview of available programs for de novo desi ign.

H-J 1998. Prediction of Binding Constants of Protein Ligands A Fast Method for the aritisation of Hits Obtained from De Novo Design or 3D Database Search Programs. Journal of nputer-Aided Molecular Design 12 309-323. 

Bohm HJ. The computer program LUDI a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Design 1992 6 61-78. 

The PepSeq program of Micromass s ProteinLynx software package was used for de novo analysis of the sequence (MS/MS) data. MS-Pattern of ProteinProspectror55 used the sequence tag determined from PepSeq to search the nonredundant database of the National Center for Biotechnology Information (NCBI) for protein identification. 

A rather provisional and "crude" version 1.0 of CHAOS was already presented at the 7th lUPAC Conference on Organic Synthesis, held at Nancy (France) in July 4-7, 1988, and some copies of it were privately distributed. The more refined version 2.0 was included in the first edition of this book. The present versions 3.0 for Macintosh and 1.0 for PC with Windows have been reprogrammed de novo and include many improvements. To those who are familiar in writing computer programs the following words (stated in a quite different context) by one of the characters of Bertolt Brecht will make sense "I m hard at work preparing my next error . 

Programs for de novo ligand design based on receptor structure... 

Hay, B.P, Firman, T.K. 2002. HostDesigner A Program for the de novo structure-based design of molecular receptors with binding sites that complement metal ion guests. Inorg. Chem. 41 (21) 5502-5512. 

---