Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment

2014 ◽  
Vol 54 (1) ◽  
pp. 324-337 ◽  
Author(s):  
Xiaohua Zhang ◽  
Sergio E. Wong ◽  
Felice C. Lightstone
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
High Performance Computing ◽  
Molecular Mechanics ◽  
Surface Area ◽  
High Performance ◽  
Massively Parallel ◽  
Generalized Born ◽  
Performance Computing

Comparing High-Performance Computing Techniques for Modeling Structural Impact on Battery Cells

2014 ◽  
Author(s):  
Mehdi Gilaki ◽  
Ilya Avdeev
Keyword(s):  
Finite Element ◽  
Parallel Processing ◽  
High Performance Computing ◽  
High Performance ◽  
Strain Curve ◽  
Thin Layers ◽  
Massively Parallel ◽  
Structural Impact ◽  
Performance Computing ◽  
Battery Cells

In this study, we have investigated feasibility of using commercial explicit finite element code LS-DYNA on massively parallel super-computing cluster for accurate modeling of structural impact on battery cells. Physical and numerical lateral impact tests have been conducted on cylindrical cells using a flat rigid drop cart in a custom-built drop test apparatus. The main component of cylindrical cell, jellyroll, is a layered spiral structure which consists of thin layers of electrodes and separator. Two numerical approaches were considered: (1) homogenized model of the cell and (2) heterogeneous (full) 3-D cell model. In the first approach, the jellyroll was considered as a homogeneous material with an effective stress-strain curve obtained through experiments. In the second model, individual layers of anode, cathode and separator were accounted for in the model, leading to extremely complex and computationally expensive finite element model. To overcome limitations of desktop computers, high-performance computing (HPC) techniques on a HPC cluster were needed in order to get the results of transient simulations in a reasonable solution time. We have compared two HPC methods used for this model is shared memory parallel processing (SMP) and massively parallel processing (MPP). Both the homogeneous and the heterogeneous models were considered for parallel simulations utilizing different number of computational nodes and cores and the performance of these models was compared. This work brings us one step closer to accurate modeling of structural impact on the entire battery pack that consists of thousands of cells.

scholarly journals Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts?

2020 ◽  
Vol 15 (9) ◽  
pp. 981-985
Author(s):  
Savíns Puertas-Martín ◽  
Antonio J. Banegas-Luna ◽  
María Paredes-Ramos ◽  
Juana L. Redondo ◽  
Pilar M. Ortigosa ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Performance Computing ◽  
High Performance ◽  
Novel Drug ◽  
Performance Computing

Editorial: High Performance Computing in Drug Discovery

2016 ◽  
Vol 17 (14) ◽  
pp. 1578-1579
Author(s):  
Horacio Pérez-Sánchez ◽  
Sandra Gesing ◽  
Ivan Merelli
Keyword(s):  
Drug Discovery ◽  
High Performance Computing ◽  
High Performance ◽  
Performance Computing

ChemInform Abstract: Hydra: A Self Regenerating High Performance Computing Grid for Drug Discovery.

ChemInform ◽  
2008 ◽  
Vol 39 (29) ◽  
Author(s):  
Drew Bullard ◽  
Alberto Gobbi ◽  
Matthew A. Lardy ◽  
Charles Perkins ◽  
Zach Little
Keyword(s):  
Drug Discovery ◽  
High Performance Computing ◽  
High Performance ◽  
Computing Grid ◽  
Performance Computing

scholarly journals Applying high-performance computing in drug discovery and molecular simulation

2016 ◽  
Vol 3 (1) ◽  
pp. 49-63 ◽  
Author(s):  
Tingting Liu ◽  
Dong Lu ◽  
Hao Zhang ◽  
Mingyue Zheng ◽  
Huaiyu Yang ◽  
...  
Keyword(s):  
Drug Discovery ◽  
High Performance Computing ◽  
Molecular Simulation ◽  
High Performance ◽  
Dynamics Simulation ◽  
Pharmaceutical Chemistry ◽  
Future Application ◽  
Chinese Government ◽  
Critical Approach ◽  
Performance Computing

Abstract In recent decades, high-performance computing (HPC) technologies and supercomputers in China have significantly advanced, resulting in remarkable achievements. Computational drug discovery and design, which is based on HPC and combines pharmaceutical chemistry and computational biology, has become a critical approach in drug research and development and is financially supported by the Chinese government. This approach has yielded a series of new algorithms in drug design, as well as new software and databases. This review mainly focuses on the application of HPC to the fields of drug discovery and molecular simulation at the Chinese Academy of Sciences, including virtual drug screening, molecular dynamics simulation, and protein folding. In addition, the potential future application of HPC in precision medicine is briefly discussed.

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