摘要
计算机辅助设计是现代药物发现的重要组成部分之一。通过使用计算方法,以提高命中识别和导联选择,提高生物利用度,并减少毒性,药物开发变得相对简便。在过去十年中积累的基因组知识的一个安装机构,为药物研究提供了巨大的机会。过去十年,基因组知识的发展为药物研究提供了巨大的机会,然而,新的挑战也出现了,因为处理这个大容量的数据需求前所未有的计算资源。另一方面,先进的异构系统提供每秒千万亿次的峰值以加速科学发现。本文回顾现代并行加速器架构,主要聚焦于英特尔Xeon Phi多核心设备。Xeon Phi是一个相对较新的平台,具有数百个计算核心和数以百计的线程。我们还讨论了针对这个加速器的常见的并行编程框架,包括MPI和OpenMP,OpenCL,HPX等。在代码开发在许多核心设备应用的最新研究进展说证明了与传统的串行计算相比异构实现的优点。本文强调选择的算法,efindsite、配体结合位点预测,用于生物分子模拟的力场和BUDE,以及基于结构的虚拟筛选机,并以此证明配备并行计算设备的异构系统可以加速药物发现的进程。
关键词: BUDE,药物的发现,efindsite,并行加速器,编程框架,Xeon Phi。
Current Drug Targets
Title:Structure-Based Drug Discovery Accelerated by Many-Core Devices
Volume: 17 Issue: 14
Author(s): Wei Feinstein and Michal Brylinski
Affiliation:
关键词: BUDE,药物的发现,efindsite,并行加速器,编程框架,Xeon Phi。
摘要: Computer-aided design is one of the critical components of modern drug discovery. Drug development is routinely streamlined using computational approaches to improve hit identification and lead selection, enhance bioavailability, and reduce toxicity. A mounting body of genomic knowledge accumulated during the last decade or so presents great opportunities for pharmaceutical research. However, new challenges also arose because processing this large volume of data demands unprecedented computing resources. On the other hand, the state-of-the-art heterogeneous systems deliver petaflops of peak performance to accelerate scientific discovery. In this communication, we review modern parallel accelerator architectures, mainly focusing on Intel Xeon Phi many-core devices. Xeon Phi is a relatively new platform that features tens of computing cores with hundreds of threads offering massively parallel capabilities for a broad range of application. We also discuss common parallel programming frameworks targeted to this accelerator, including OpenMP, OpenCL, MPI and HPX. Recent advances in code development for many-core devices are described to demonstrate the advantages of heterogeneous implementations over the traditional, serial computing. Finally, we highlight selected algorithms, eFindSite, a ligand binding site predictor, a force field for bio-molecular simulations, and BUDE, a structure-based virtual screening engine, to demonstrate how modern drug discovery is accelerated by heterogeneous systems equipped with parallel computing devices.
Export Options
About this article
Cite this article as:
Wei Feinstein and Michal Brylinski , Structure-Based Drug Discovery Accelerated by Many-Core Devices, Current Drug Targets 2016; 17 (14) . https://dx.doi.org/10.2174/1389450117666160112112854
DOI https://dx.doi.org/10.2174/1389450117666160112112854 |
Print ISSN 1389-4501 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-5592 |
Call for Papers in Thematic Issues
New drug therapy for eye diseases
Eyesight is one of the most critical senses, accounting for over 80% of our perceptions. Our quality of life might be significantly affected by eye disease, including glaucoma, diabetic retinopathy, dry eye, etc. Although the development of microinvasive ocular surgery reduces surgical complications and improves overall outcomes, medication therapy is ...read more
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
Related Articles
-
Natural Compounds Therapeutic Features in Brain Disorders by Experimental, Bioinformatics and Cheminformatics Methods
Current Medicinal Chemistry Subtracting Gene Function by Gene Silencing and Disruption in Bacteria
Current Biotechnology Hodgkin Lymphoma in HIV Positive Patients
Current HIV Research NMR Based Metabolomics: An Exquisite and Facile Method for Evaluating Therapeutic Efficacy and Screening Drug Toxicity
Current Topics in Medicinal Chemistry Inhalation Delivery of Host Defense Peptides (HDP) using Nano- Formulation Strategies: A Pragmatic Approach for Therapy of Pulmonary Ailments
Current Protein & Peptide Science Effectiveness of Antiretroviral Therapy in HIV-1-Infected Active Drug Users Attended in a Drug Abuse Outpatient Treatment Facility Providing a Multidisciplinary Care Strategy
Current HIV Research CYP1A2, CYP2A6, CYP2B6, CYP3A4 and CYP3A5 Polymorphisms in Two Bantu-Speaking Populations from Cameroon and South Africa: Implications for Global Pharmacogenetics
Current Pharmacogenomics and Personalized Medicine Innate T-Cell Immunity in HIV Infections: The Role of Vg9Vd2 T Lymphocytes
Current Molecular Medicine Computational Methods for Protein-Protein Interaction and their Application
Current Protein & Peptide Science Metal Complexes, their Cellular Targets and Potential for Cancer Therapy
Current Pharmaceutical Design Adverse Drug Reactions to Anti-TB Drugs: Pharmacogenomics Perspective for Identification of Host Genetic Markers
Current Drug Metabolism Ascorbic Acid: Its Role in Immune System and Chronic Inflammation Diseases
Mini-Reviews in Medicinal Chemistry Advances and Application of DNA-functionalized Nanoparticles
Current Medicinal Chemistry Modulation of Cytokine Network in the Comorbidity of Schizophrenia and Tuberculosis
Current Topics in Medicinal Chemistry Neuropeptides as Therapeutic Approach to Autoimmune Diseases
Current Pharmaceutical Design Specific Targeting of Engineered Nanoparticles to Activated Macrophages
Current Nanoscience Heat Shock Protein-60 and Risk for Cardiovascular Disease
Current Pharmaceutical Design Estrogen Receptor Beta (ERβ) Expression in Different Subtypes of Malignant Pleural Mesothelioma
Current Respiratory Medicine Reviews Benzothiazole-based Compounds in Antibacterial Drug Discovery
Current Medicinal Chemistry Targeting Tuberculosis: A Glimpse of Promising Drug Targets
Mini-Reviews in Medicinal Chemistry