MC

HOOK [71] linker search for fragments placed by MCSS ... 

Application developed by using a Fisons GC 8000 chi omatogi aph where the two columns were installed and coupled via a moving capillary stream switching (MCSS) system. The chi omatogi aph was equiped with a flame-ionization detector on the MCSS system outlet and a Flame-photometric detector on the main column outlet, and a split/splitless injector. 

A fault tree is, itself, a Boolean equation relating basic events to the top event. The equation can be analyzed quantitatively or qualitatively by hand or by using computer code(s). If it is analyzed quantitatively, the probabilities or frequencies of the intermediate events and the top event are calculated. If it is analyzed qualitatively, a list of the failure combinations that can cause the top event is generated. These combinations are known as cut sets. A minimal cut set (MCS) is the smallest combination of basic events that, if they occur or exist simultaneously, cause the top event. These combinations are termed "minimal" because all of the basic events in a MCS must occur if the top event is to occur. Thus, a list of MCSs represents the known ways the top event can occur, stated in terms of equipment failures, human errors, and associated circumstances. 

Schematic representation of the MCSS procedure. Conditional statements are enclosed by diamonds.

Aliphatic and aromatic fragments do not bear any partial charges in the polar-hydrogen approximation. Hence, MCSS determines their optimal position in the... 

Stereo view of the sixty propane minima (thick lines) obtained with the modified force field (see text) on the surface of the A peptide chain (medium lines) of the GCN4 leucine zipper (PDB code 2ZTA). Although the peptide chain was removed during the MCSS procedure, its backbone and hydrophobic side chains are also drawn (thin lines) to show how the propane minima match the aliphatic groups of chain B. Hydrophobic residues are labeled at their Ca atom.Five clusters of propane minima that do not match the hydrophobic side chain of the helix involved in the interhelical interactions are labeled from A (top right) to E (bottom center) and discussed in the text. 

The inhibitor PPACK is also shown (medium lines), though it was removed during the MCSS procedure. Some Ca atoms of thrombin are labeled. 

A somewhat different approach has been implemented in MCSS (multiple copies simultaneous search) [10]. In this method, up to 5000 copies of a functional group are randomly distributed in the binding pocket and simultaneously minimized by a force field. The simultaneous optimization is performed in... 

Rarey, M., Kramer, B., Lengauer, T., Klebe, G. A fast flexible docking method using an incremental construction algorithm. /. Mol. Biol. 1996, 263, 470-489. Joseph-McCarthy, D., Alvarez, J.C. Automated generation of MCSS-derived phar-macophoric DOCK site points for searching multiconformation databases. Proteins 2003, 53, 189-202. 

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