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Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations.用于分子动力学模拟中短程力计算的基于现场可编程门阵列(FPGA)的协处理器的显式设计
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Studies of folding and misfolding using simplified models.使用简化模型对折叠和错误折叠的研究。
Curr Opin Struct Biol. 2006 Feb;16(1):79-85. doi: 10.1016/j.sbi.2006.01.001. Epub 2006 Jan 18.
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Simple but predictive protein models.简单但具有预测性的蛋白质模型。
Trends Biotechnol. 2005 Sep;23(9):450-5. doi: 10.1016/j.tibtech.2005.07.001.
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Docking and scoring in virtual screening for drug discovery: methods and applications.药物发现虚拟筛选中的对接与评分:方法与应用
Nat Rev Drug Discov. 2004 Nov;3(11):935-49. doi: 10.1038/nrd1549.
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Multiple grid methods for classical molecular dynamics.经典分子动力学的多重网格方法
J Comput Chem. 2002 Apr 30;23(6):673-84. doi: 10.1002/jcc.10072.
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Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.分子表面识别:通过相关技术测定蛋白质与其配体之间的几何契合度。
Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2195-9. doi: 10.1073/pnas.89.6.2195.

基于现场可编程门阵列(FPGA)的加速器的计算模型

Computing Models for FPGA-Based Accelerators.

作者信息

Herbordt Martin C, Gu Yongfeng, Vancourt Tom, Model Josh, Sukhwani Bharat, Chiu Matt

机构信息

Boston University.

出版信息

Comput Sci Eng. 2008 Oct 17;10(6):35-45. doi: 10.1109/MCSE.2008.143.

DOI:10.1109/MCSE.2008.143
PMID:21603152
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3096930/
Abstract

Field-programmable gate arrays are widely considered as accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. FPGA computing enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using these computing models in developing FPGA applications for molecular modeling.

摘要

现场可编程门阵列被广泛认为是计算密集型应用的加速器。FPGA应用开发的一个关键阶段是找到并映射到合适的计算模型。FPGA计算支持具有高度灵活的细粒度并行性和诸如广播和集体响应等关联操作的模型。几个案例研究证明了在开发用于分子建模的FPGA应用中使用这些计算模型的有效性。