DOCK program

Strynadka et al., 1996] Strynadka, N., Eisenstein, M., Katchalski-Katzir, E., Shoichet, B., Kuntz, I., Abagyan, R., Totrov, M., Janin, J., Cherflls, J., Zimmerman, F., Olson, A., Duncan, B., Rao, M., Jackson, R., Sternberg, M., and James, M. Molecular docking programs successfully predict the binding of a /3-lactamase inhibitory protein to TEM-1 /3-lactamase. Nature Struct. Biol. 3 (1996) 233-239... 

An overview of docking programs is given in Tabic 10.4-3. Depending on the way the conformational flexibility of the ligand is treated, docking can be either rigid or flexible. 

Fig. 12.23 Two simple scoring functions used in docking. On the left is the basic scoring scheme used by the DOCK program [Desjarlais et al. 1988], On the right is the piecewise linear potential [Cclhaar et al. 1995],...

FlexX An extension of the FlexX docking program which increases the efficiency of the docking of combinatorial libraries Tripos, Inc. http //www.tripos.com [32]... 

Makino S, Ewing TJ, Kuntz ID. DREAM-r-i- flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des 1999 13 513-32. 

Burkhard P, Hommell U, Sanner M, Walkinshaw MD. The discovery of steroids and other novel FKBP inhibitors using a molecular docking program. J Mol Biol 1999 287 853-8. 

Docking and target structure-based database searches, 6 13-14 DOCK program, 6 13 10 337-338 5,13-Docosadienoic acid, physical properties, 5 33t... 

Table 3.2 Most commonly used molecular docking programs [22]...

Making, S., Ewing, T.J.A., Kuntz, I.D. DREAM4—p Flexible docking program for virtual combinatorial libraries. 

Normally, programs for virtual screening, for example, docking software, do not take multiple hydrogen placements of these three types into account. There are, however, a few partial solutions. The docking program FlexX [11] can generate stereoisomers on... 

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