Docking Scoring

The calculation of the binding affinity with con.sidcration of all tbc.se effects for virtual screening is not possible. In order to circumvent thus difficulty, scoring functions arc used instead, c.g., the Liidi scoring function [80, or consensus scoring functions derived from FlevX score, DOCK score, GOLD score, ChemScore, or PMF score [81 ]. 

Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 2000 43 4759-67. 

Keywords VS, Virtual Screening, Lead discovery, lead, HTS, Pharmacophore-Based, Structure-Based, Fragment-based, Ligand-based, Docking, Scoring, hybrid workflows, VS strategy, Benchmarking VS... 

One or more lead molecules may be used as a focusing target. Similarity metrics include Daylight fingerprint Tanimoto similarity. The penalty score for each compound in the library is defined as the distance between it and the most similar lead molecule. The penalty score for the library is the average of the individual compound penalty scores. QSAR predictions and docking scores can also be used in this term. 

Basis products (BPs) Exploits the redundancy of fragments in a combinatorial library and identifies a small subset of compounds (BPs) which represent the entire virtual library. BPs are docked, scored, and used for final library enumeration (85)... 

Each of the sixteen compounds was tested for GAPDH inhibition (Table 7). Half of them were inactive while the other ones showed inhibition in a range between 1.2 and 25 mM Unfortunately, there appears to be no correlation between the DOCK scores and the IC50 values. For examples, norepinephrine and... 

Bissantz, C., Folkers, G., Rognan, D. Protein-based Virtual Screening of Chemical Databases 1. Evaluation of Different Docking/Scoring Combina-... 

Many strategies have been proposed to enrich a set of molecules with active compounds by virtual screening similarity search [49], docking-scoring [50], QSAR [51] and, of course, pharmacophore models. This section reviews some methods that can be applied to any of those approaches. 

Figure 2.146. The Maestro interface includes tools for structure visualization and data analsysis. Here, Maestro illustrates a ligand (green) docked to stromelysin (orange ribbons and white surafce). The docking scores of a series of stromelysin inhibitors have been plotted within Maestro s project facility.

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