… It is an ideal situation that does not reflect real-world docking experiments where the receptor
structure is obtained from complexes with other inhibitors (ie, non-native conformations), …

… In this article, we use the DUD-E database to perform a benchmark of four of the most popular
docking programs [18], Gold [19], Glide [20], Surflex [21] and FlexX [22]. Our key objective …

… ability of a docking program to find a well docked complex with respective experimental
crystal structure as the top-ranked pose, which is crucial for docking programs especially used …

… which adequately explains its use to the average chemist. … workflow using Surflex-Dock to
perform the same docking analysis … and Surflex-Dock, has shown a good level of performance. …

… Some conclusions of these docking benchmarks seem to be in contradiction with our …
Similarly to our recommendations for VS [26], we recommend for docking the use of several …

… performance correlations between eSim and Surflex-Dock using single and ensemble
targets were lower than those seen between the best alternative docking … estimate of real-world …

… Electively, some elite standards defined by the user automatically select superior … application
has been used widely in molecular docking since 1997 (Genetic algorithms and their use in …

… in benchmarking databases as well as current benchmarking … for the selection and the
design of benchmarking datasets. … Application to high-throughput docking on metabotropic …

… examples, comparison of performance for existing tools and algorithms, state of art in docking,
… since the underlying algorithms are just approximations of the real world. So, a number of …

… based on their ease of use, suitability for large-scale analysis, and performance on previous
… better performance on benchmarking studies. Docking solutions from each program are …