| 1. |
- Gorgen, Ralph, et al.
(författare)
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CONTREX : Design of embedded mixed-criticality CONTRol systems under consideration of EXtra-functional properties
- 2016
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Ingår i: 19TH EUROMICRO CONFERENCE ON DIGITAL SYSTEM DESIGN (DSD 2016). - : IEEE. - 9781509028160 ; , s. 286-293
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Konferensbidrag (refereegranskat)abstract
- The increasing processing power of today's HW/SW platforms leads to the integration of more and more functions in a single device. Additional design challenges arise when these functions share computing resources and belong to different criticality levels. The paper presents the CONTREX European project and its preliminary results. CONTREX complements current activities in the area of predictable computing platforms and segregation mechanisms with techniques to consider the extra-functional properties, i.e., timing constraints, power, and temperature. CONTREX enables energy efficient and cost aware design through analysis and optimization of these properties with regard to application demands at different criticality levels.
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| 2. |
- Markidis, Stefano, et al.
(författare)
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Understanding the I/O Impact on the Performance of High-Throughput Molecular Docking
- 2021
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Ingår i: Proceedings of PDSW 2021: IEEE/ACM 6th International Parallel Data Systems Workshop, Held in conjunction with SC 2021: The International Conference for High Performance Computing, Networking, Storage and Analysis. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 9-14
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Konferensbidrag (refereegranskat)abstract
- High-throughput molecular docking is a data-driven simulation methodology to estimate millions of molecules' position and interaction strength (ligands) when interacting with a given protein site. Because of its data-driven nature, the high-throughput molecular docking performance depends on how fast we can ingest data into the processing pipeline and how efficiently we can write molecular docking results to a shared file. This work characterizes the I/O performance of a high-performance, high-throughput molecular docking application, called Docker-HT, running on a supercomputer up to 512 computing nodes with two different parallel I/O configurations. We show that a tuned I/O configuration can improve the overall parallel efficiency from 71% to 90% on 512 nodes and identify and solve a performance degradation observed when running on 16 and 32 nodes.
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| 3. |
- Natarajan Arul, Murugan, et al.
(författare)
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A Review on Parallel Virtual Screening Softwares for High-Performance Computers
- 2022
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Ingår i: Pharmaceuticals. - : MDPI AG. - 1424-8247. ; 15:1, s. 63-
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Forskningsöversikt (refereegranskat)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(6) to 10(12)), 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.
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| 4. |
- Vistoli, Giulio, et al.
(författare)
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MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions
- 2023
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Ingår i: Expert Opinion on Drug Discovery. - : Taylor and Francis Ltd.. - 1746-0441 .- 1746-045X. ; 18:8, s. 821-833
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Collaborative computing has attracted great interest in the possibility of joining the efforts of researchers worldwide. Its relevance has further increased during the pandemic crisis since it allows for the strengthening of scientific collaborations while avoiding physical interactions. Thus, the E4C consortium presents the MEDIATE initiative which invited researchers to contribute via their virtual screening simulations that will be combined with AI-based consensus approaches to provide robust and method-independent predictions. The best compounds will be tested, and the biological results will be shared with the scientific community. Areas covered: In this paper, the MEDIATE initiative is described. This shares compounds’ libraries and protein structures prepared to perform standardized virtual screenings. Preliminary analyses are also reported which provide encouraging results emphasizing the MEDIATE initiative’s capacity to identify active compounds. Expert opinion: Structure-based virtual screening is well-suited for collaborative projects provided that the participating researchers work on the same input file. Until now, such a strategy was rarely pursued and most initiatives in the field were organized as challenges. The MEDIATE platform is focused on SARS-CoV-2 targets but can be seen as a prototype which can be utilized to perform collaborative virtual screening campaigns in any therapeutic field by sharing the appropriate input files.
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