AutoDock Vina(Vina)is a widely adopted molecular docking tool,often regarded as a standard or used as a baseline in numerous studies.However,its computational process is highly time-consuming.The pioneering field-prog...AutoDock Vina(Vina)is a widely adopted molecular docking tool,often regarded as a standard or used as a baseline in numerous studies.However,its computational process is highly time-consuming.The pioneering field-programmable gate array(FPGA)-based accelerator of Vina,known as Vina-FPGA,offers a high energy-efficiency approach to speed up the docking process.However,the computation modules in the Vina-FPGA design are not efficiently used.This is due to Vina exhibiting irregular behaviors in the form of nested loops with changing upper bounds and differing control flows.Fortunately,Vina employs the Monte Carlo iterative search method,which requires independent computations for different random initial inputs.This characteristic provides an opportunity to implement further parallel computation designs.To this end,this paper proposes Vina-FPGA2,an inter-module pipeline design for further accelerating Vina-FPGA.First,we use individual computational task(Task)independence by sequentially filling Tasks into computation modules.Then,we implement an inter-module pipeline parallel design by the Tag Checker module and architectural modifications,named Vina-FPGA2-Baseline.Next,to achieve resource-efficient hardware implementation,we describe it as an optimization problem and develop a reinforcement learning-based solver.Targeting the Xilinx UltraScale XCKU060 platform,this solver yields a more efficient implementation,named Vina-FPGA2-Enhanced.Finally,experiments show that Vina-FPGA2-Enhanced achieves an average 12.6×performance improvement over the central processing unit(CPU)and a 3.3×improvement over Vina-FPGA.Compared to Vina-GPU,Vina-FPGA2 achieves a 7.2×enhancement in energy efficiency.展开更多
The Vinaya School is a school of Buddhism in China, of which the main object was the study, the propagation and the observance of the Vinaya rules. Its basic scripture was the Four-division-vinaya(or the Dharmaguptaka...The Vinaya School is a school of Buddhism in China, of which the main object was the study, the propagation and the observance of the Vinaya rules. Its basic scripture was the Four-division-vinaya(or the Dharmaguptaka-vinaya Sifenlü 四分律), one of the five classes of the Vinaya works, and so it was also known as the School of the Four-division-vinaya.展开更多
先导化合物发现是创新药物研发的最重要环节之一。针对目前海量功能不明确的小分子化合物,本文构建了一个用来实现快速发现先导化合物,有效降低药物研发成本的计算机辅助药物筛选平台。该平台采用分布式架构思想,集成了Auto Dock Vina...先导化合物发现是创新药物研发的最重要环节之一。针对目前海量功能不明确的小分子化合物,本文构建了一个用来实现快速发现先导化合物,有效降低药物研发成本的计算机辅助药物筛选平台。该平台采用分布式架构思想,集成了Auto Dock Vina和多个小分子库,具有数据安全、计算与存储的负载均衡以及实时监控的特点。应用平台进行先导化合物筛选,在较短时间发现了有针对性的活性小分子化合物,命中率高,大大缩短先导化合物发现周期。该平台具有很好的实用性和良好的扩展性。展开更多
靶标确证是老药新用、药物毒副作用研究的关键。基于分子对接方法 Auto Dock Vina和内部构建的疾病靶标数据库,采用分布式架构,构建了反向虚拟筛选平台。应用该平台对药物吡斯的明进行靶标确证,最终成功找到其靶标乙酰胆碱酯酶,验证了...靶标确证是老药新用、药物毒副作用研究的关键。基于分子对接方法 Auto Dock Vina和内部构建的疾病靶标数据库,采用分布式架构,构建了反向虚拟筛选平台。应用该平台对药物吡斯的明进行靶标确证,最终成功找到其靶标乙酰胆碱酯酶,验证了平台的实用性和准确性。展开更多
Ulcer is one of the life threatening diseases. It is an open sore on an external or internal surface of the body caused by a break in the skin or mucous membrane which fails to heal. In this work, specific ligands tha...Ulcer is one of the life threatening diseases. It is an open sore on an external or internal surface of the body caused by a break in the skin or mucous membrane which fails to heal. In this work, specific ligands that are suitable for ulcer have been studied computationally. Docking of the triterpenoids of Lonchocarpus cyanescens with target proteins of PDB codes 1AFC, 1AXM and 2AXM were performed using AutoDock Vina and Pymol for docking and post-docking analysis, respectively. In this study, the triterpenoid ligands with binding affinity/inhibitory constants -7.2/5.21, -6.5/16.99 and -6.2/28.20 for OH, and -6.7/12.12, -6.3/23.82 and -6.1/33.40 for OCH3 were compared with the standard ligands. Our study indicates that the results corresponding to triterpenoid ligands are close to standard ligands.展开更多
基金Project supported by the National Natural Science Foundation of China(No.92464301)the Big Data Computing Center of Southeast University。
文摘AutoDock Vina(Vina)is a widely adopted molecular docking tool,often regarded as a standard or used as a baseline in numerous studies.However,its computational process is highly time-consuming.The pioneering field-programmable gate array(FPGA)-based accelerator of Vina,known as Vina-FPGA,offers a high energy-efficiency approach to speed up the docking process.However,the computation modules in the Vina-FPGA design are not efficiently used.This is due to Vina exhibiting irregular behaviors in the form of nested loops with changing upper bounds and differing control flows.Fortunately,Vina employs the Monte Carlo iterative search method,which requires independent computations for different random initial inputs.This characteristic provides an opportunity to implement further parallel computation designs.To this end,this paper proposes Vina-FPGA2,an inter-module pipeline design for further accelerating Vina-FPGA.First,we use individual computational task(Task)independence by sequentially filling Tasks into computation modules.Then,we implement an inter-module pipeline parallel design by the Tag Checker module and architectural modifications,named Vina-FPGA2-Baseline.Next,to achieve resource-efficient hardware implementation,we describe it as an optimization problem and develop a reinforcement learning-based solver.Targeting the Xilinx UltraScale XCKU060 platform,this solver yields a more efficient implementation,named Vina-FPGA2-Enhanced.Finally,experiments show that Vina-FPGA2-Enhanced achieves an average 12.6×performance improvement over the central processing unit(CPU)and a 3.3×improvement over Vina-FPGA.Compared to Vina-GPU,Vina-FPGA2 achieves a 7.2×enhancement in energy efficiency.
文摘The Vinaya School is a school of Buddhism in China, of which the main object was the study, the propagation and the observance of the Vinaya rules. Its basic scripture was the Four-division-vinaya(or the Dharmaguptaka-vinaya Sifenlü 四分律), one of the five classes of the Vinaya works, and so it was also known as the School of the Four-division-vinaya.
文摘先导化合物发现是创新药物研发的最重要环节之一。针对目前海量功能不明确的小分子化合物,本文构建了一个用来实现快速发现先导化合物,有效降低药物研发成本的计算机辅助药物筛选平台。该平台采用分布式架构思想,集成了Auto Dock Vina和多个小分子库,具有数据安全、计算与存储的负载均衡以及实时监控的特点。应用平台进行先导化合物筛选,在较短时间发现了有针对性的活性小分子化合物,命中率高,大大缩短先导化合物发现周期。该平台具有很好的实用性和良好的扩展性。
文摘Ulcer is one of the life threatening diseases. It is an open sore on an external or internal surface of the body caused by a break in the skin or mucous membrane which fails to heal. In this work, specific ligands that are suitable for ulcer have been studied computationally. Docking of the triterpenoids of Lonchocarpus cyanescens with target proteins of PDB codes 1AFC, 1AXM and 2AXM were performed using AutoDock Vina and Pymol for docking and post-docking analysis, respectively. In this study, the triterpenoid ligands with binding affinity/inhibitory constants -7.2/5.21, -6.5/16.99 and -6.2/28.20 for OH, and -6.7/12.12, -6.3/23.82 and -6.1/33.40 for OCH3 were compared with the standard ligands. Our study indicates that the results corresponding to triterpenoid ligands are close to standard ligands.
