Virtual Laboratory: Enabling On-Demand Drug Design with the World Wide Grid

A Review on Parallel Virtual Screening Softwares for High Performance Computers

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 bindi…

GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis

COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preliminary phases by using computer simulations. In particular, virtual screening is an in-silico phase that is needed to filter a large set of possible drug candidates to a manageable number. This paper presents the implementations and a comparative analysis of two GPU-optimized implementations of a virtual screening algorithm targeting novel GPU architectures. The first adopts a traditional approach that spreads the co…

用于管理计算实验的虚拟实验室

A Virtual Laboratory for Managing Computational Experiments

针对计算实验规模与复杂性增加导致的可重复性与元数据管理难题，本文提出了虚拟实验室SCHEMA lab，通过捕获实验配置和性能指标等丰富元数据并管理实验全生命周期，显著提升了计算研究的可重复性与效率。

Improving computation efficiency using input and architecture features for a virtual screening application

Virtual screening is an early stage of the drug discovery process that selects the most promising candidates. In the urgent computing scenario it is critical to find a solution in a short time frame. In this paper, we focus on a real-world virtual screening application to evaluate out-of-kernel optimizations, that consider input and architecture features to improve the computation efficiency on GPU. Experiment results on a modern supercomputer node show that we can almost double the performance. Moreover, we implemented the optimization using SYCL and it provides a consistent benefit with the …

百亿亿次级可调节、可移植的超大规模药物发现平台：LIGATE方法

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach

LIGATE整合欧洲一流CADD组件与Exascale超算资源，提出自动化、可移植的超大规模虚拟筛选工作流，以高速度、高精度在数天内完成药物发现活动。

Implementation of functions in R tool in parallel environment

Drug promiscuity and polypharmacology are much discussed topics in pharmaceutical research. Drug repositioning applies established drugs to new disease indications with increasing success. As polypharmacology, defined a drug's ability to bind to several targets but due to possible side effects, this feature is not taken into consideration. Thus, the pharmaceutical industry focused on the development of highly selective single-target drugs. Nowadays after lot of researches, it is clear that polypharmacology is important for the efficacy of drugs. There are side effects but on the other hand, th…