Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding – Consensus and Caveats

Publisher Summary This chapter provides a background, describes various methods, performance measurements, evaluations, post-processing, and the future directions of high throughput docking methods for pharmaceutical lead finding. The docking programs generate poses for each candidate ligand, a pose being defined by the ligand conformation plus orientation within the binding site. Selecting among available software for high throughput docking (HTD) is a challenging problem. HTD studies usually assume a rigid protein because allowing for a flexible protein would be too computationally expensive. Cole et al suggest that the statistical significance of HTD results must be established if the data are to be interpreted with any certainty. It is clear that a significant amount of time has gone into this recent round of HTD evaluations, on the part of both the industrial practitioners and also the academic and commercial developers, who understandably wanted to ensure that their programs are deployed in optimal fashion. In the interest of reducing time spent on future evaluations, it would be useful to establish a standardized set of benchmarks, such as the ones employed by computer hardware vendors.

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