Abstract
Drug discovery is the most expensive, time-demanding, and challenging project in biopharmaceutical companies which aims at the identification and optimization of lead compounds from large-sized chemical libraries. The lead compounds should have high-affinity binding and specificity for a target associated with a disease, and, in addition, they should have favorable pharmacodynamic and pharmacokinetic properties (grouped as ADMET properties). Overall, drug discovery is a multivariable optimization and can be carried out in supercomputers using a reliable scoring function which is a measure of binding affinity or inhibition potential of the drug-like compound. The major problem is that the number of compounds in the chemical spaces is huge, making the computational drug discovery very demanding. However, it is cheaper and less time-consuming when compared to experimental high-throughput screening. As the problem is to find the most stable (global) minima for numerous protein–ligand complexes (on the order of 10 to 10), the parallel implementation of in silico virtual screening can be exploited to ensure drug discovery in affordable time. In this review, we discuss such implementations of parallelization algorithms in virtual screening programs. The nature of different scoring functions and search algorithms are discussed, together with a performance analysis of several docking softwares ported on high-performance computing architectures.
Highlights
A Review on Parallel Virtual Screening Softwares forNatarajan Arul Murugan 1, *,† , Artur Podobas 1 , Davide Gadioli 2 , Emanuele Vitali 2 , Gianluca Palermo 2 and Stefano Markidis 1, *
Drug discovery is one of the most highly challenging, time-consuming and expensive projects in the healthcare sector
MPAD4 [57] is a parallel implementation of Autodock4.0, and the important features when compared to parent code are listed as follows: (i) It uses MPI to distribute docking jobs across the cluster; (ii) The grid maps generated for receptor are reused for all the docking calculations while in the default version, and these files are generated for each ligand docking with the target receptor and loaded into memory and released at the completion of docking
Summary
Natarajan Arul Murugan 1, *,† , Artur Podobas 1 , Davide Gadioli 2 , Emanuele Vitali 2 , Gianluca Palermo 2 and Stefano Markidis 1, *.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have