Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher
evopro Informatics and Automation Ltd, Budapest, Hungary
Chapter 6 in the book "Bioinformatics", book edited by Horacio Perez-Sanchez, Intechopen, 2012


   title={Hardware Accelerated Molecular Docking: A Survey},

   author={Pechan, I. and Feh{‘e}r, B.},



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Hardware acceleration is the general concept of applying a specialized hardware for a given problem instead of an ordinary CPU in order to get lower processing time. General purpose CPUs can be considered as a totally general platform suitable for executing virtually any software or algorithm. Application specific accelerators have a custom architecture that fits the needs of a certain family of algorithms. As a consequence, they are able to outperform CPUs by orders of magnitude in a special application area but they are unfit for other, more general tasks. In contrast to normal CPUs, which are essentially serial machines executing instructions sequentially, hardware accelerators use parallel architectures which allow them to exploit the parallelism available in the given application by performing independent operations simultaneously. The most important examples of hardware accelerators are graphics processing units (GPUs) and field-programmable gate array devices (FPGAs). GPUs are special many-core processors optimized for 3D rendering and image processing purposes. GPU devices are nowadays part of any desktop PC configurations and they can be programmed with general purpose programming languages. These facts make them an easily accessible and costeffective accelerator platform and explain why they are used more and more frequently even in applications that are not graphics-related (general purpose GPU programming). FPGAs are programmable logic devices consisting of hundreds of thousands of general logic elements whose interconnection can be configured by the user. Thus FPGAs have a highly flexible architecture that allows to implement a totally custom digital hardware without the enormous cost of designing and manufacturing an application-specific integrated circuit (ASIC). When using an FPGA as a hardware accelerator a custom logic device is realized in the FPGA whose only purpose is to execute the algorithm to be accelerated as effectively as possible; thus the algorithm is usually implemented as pure hardware instead of software.
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