Recent Advances and Future Trend on the Emerging Role of GPUs as Platforms for Virtual Screening-Based Drug Discovery [chapter]

Horacio Prez-Snchez, Jos M., Jos M.
2012 Virtual Screening  
2 Will-be-set-by- IN-TECH of existing VS programs is to move into the direction of established all-atom biophysical simulation. Both better scoring functions and novel docking strategies will contribute in this direction. But one of the main problems in this direction is that all VS methods mentioned previously were developed for and run on commodity PCs, with its limitations in terms of availability of computing power. However, current PCs are becoming powerful desktop machines with beyond a
more » ... raflop available on them, thanks to the availability of GPUs as an underlying hardware for developing general-purpose applications. We report and show how combining accurate and transferable biophysical VS techniques with these modern massively parallel hardware, allowing significant steps towards more accurate VS screening methods. Driven by the demand of the game industry, Graphics Processing Units (GPUs) have completed a steady transition from mainframes to workstations to PC cards, where they emerge nowadays like a solid and compelling alternative to traditional computing platforms, delivering extremely high floating point performance and massively parallelism at a very low cost, and thus promoting a new concept of the High Performance Computing (HPC) market; i.e. high performance desktop computing. This fact has attracted many researchers and encouraged the use of GPUs in a broader range of applications, where developers are required to leverage this technology with new programming models which ease the developer's task of writing programs to run efficiently on GPUs (Garland et al., 2008).
doi:10.5772/35169 fatcat:3rzpjwks4zbxhosbegqy5q73ti