Docking benchmarks

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

Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49 6789-6801... 

Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2354 52 88-91. 

The first test usually performed with a docking tool is the reproduction of complexes with known structures. The results achieved with docking algorithms are quite difficult to compare for several reasons. First, there is no unique benchmark set and every method is published with a small set of test results only. Second, different levels of a priori knowledge are used in the preparation of the input data and in the calculation. Examples for a priori knowledge are the definition of the active site, the placement of polar... 

There are still many unsolved problems in computational chemistry and, as discussed, many of them are not new. We still need a method for the quick and accurate calculation of free energies, and we need to understand the limits on the accuracy of any predictive methods. More broadly, what confidence limits can we put on any given prediction from any given level of theory For virtual screening, what are the most important terms left out of the standard docking functions, and indeed higher simulation methods Can we imagine a set of widely accepted well-validated model systems and benchmarks, both for experiment and theory ... 

Horizonting and orienting in element-coordinates of instruments used to set out and survey-in took place using the benchmarks put on the element roof while in construction dock. Position and height of reflectors were checked by relative measurements between them or trough measurements from a different station. To calculate the amount of ballast needed, freeboard was measured for each element. 

Spitzer R, Jain AN. Surflex-dock Docking benchmarks and real-world application. J Comput Aided Mol Design 2012 26(6) 687-699. 

Damm-Ganamet KL, Smith RD, Dunbar JB, Stuckey JA, Carlson HA (2013) CSAR benchmark exercise 2011-2012 evaluation of results from docking and relative ranking of blinded congeneric series. J Chem Inf Model. doi 10.1021/ci400025f... 

Mintseris, J.> Wiehe> K.> Pierce, B.> Anderson, R., Chen, R., Janin, J., Weng, Z. (2005). Protein-protein docking benchmark 2.0 An update. Proteins Structure, Function, and Bioinformatics, 60, 214. 

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