Energy scoring

Rognan published the scoring function FRESNO (fast free energy scoring function), which considers a hydrogen-bond term, a lipophilic terra, a repulsive term for the buried polar surface, a rotational term, and a desolvation terra [82]. 

As shown in Figure 2, when a herbmore eats a plant, only about 10 percent of the energy scored in that plant is converted to animal biomass the rest is used up in everyday activities. The same is true for each succeeding trophic level. Note that the commonly cited 10 percent energy transfer figure is... 

Figure 9.12 Plot of observed activity versus energy score for compounds sampling the SV pocket of BACE-1. ( ) Compounds containing amine reagents which were incorporated prior to the study (m) compounds containing amine reagents selected independent of the scoring iaj compounds containing amine reagents selected based on scoring.

Figure 9.12). In addition, our arbitrary cut-off for the energy score may have missed some interesting inhibitors, e.g. the ethyl- and isobutylamines which are labeled as Below cutoff in Figure 9.12. However, the score versus activity trend is clear, including a true negative control, the tert-butylamine reagent, which was predicted (and subsequently observed) to yield an inhibitor with very low BACE-1 activity. In addition to demonstrating the utility of an in situ virtual reagent selection, this study served to validate the hypothesis that the BACE-1 SF pocket is large, open and promiscuous, as a variety of reagents led to potent BACE-1 inhibitors.

SIFt scoring approach. For p38, the 11ybrid Scoring scheme (p-SIFT to rule out undesirable poses followed by energy scoring function identify and rank the best pose) was found to offer no improvement in enrichment over that obtained from using p-SIFt scoring. 

Docking poses generated by AutoDock, GOLD, and FlexX can be easily pooled and/or rescored with SCORE (21), the three scoring functions available in the X-SCORE program (22), and/or user-defined scoring functions. This can be achieved via simple scripts that extract the relevant information from the various output files (an example of such a script is available from the authors upon request). When the results are saved in a format readable to SYBYL (i.e., tab-separated columns), the energy scores can be listed and imported into a SYBYL spreadsheet ... 

A spreadsheet is opened with all structures ranked in a column. Select all rows with conformations and add energy scores ... 

The energy scoring component of DOCK [55-57] is also based on the implementation of force field scoring. The program offers the possibility of precomputing the van der Waals and electrostatic potentials for the receptor and... 

The mean-force scoring functions based upon an atom-randomized reference state use the method for the simple monatomic system to calculate p (r). In this method, it is assumed that all the atoms are randomly placed in the system without interatomic interactions, ignoring interatomic connectivity, excluded volume, and other factors in the structures of protein-ligand complexes. The resulted pair potentials w,y are then taken as the true potentials Uy despite their differences, and the binding energy score is calculated as... 

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