scholarly journals An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1693 ◽  
Author(s):  
Maral Aminpour ◽  
Carlo Montemagno ◽  
Jack A. Tuszynski
Keyword(s):  
Drug Discovery ◽  
Small Molecules ◽  
High Performance ◽  
Current Status ◽  
General Area ◽  
Dna Translocation ◽  
Computer Aided Drug Design ◽  
Major Significance ◽  
In Silico Modeling ◽  
Performance Computing

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Current Status on High Performance Computing for Vehicle Aerodynamics Using Large Eddy Simulation

2007 ◽  
Author(s):  
Makoto Tsubokura ◽  
Takuji Nakashima ◽  
Nobuyuki Oshima ◽  
Kozo Kitoh ◽  
Huilai Zhang ◽  
...  
Keyword(s):  
Large Eddy Simulation ◽  
High Performance ◽  
Current Status ◽  
Navier Stokes ◽  
Eddy Simulation ◽  
The Earth ◽  
Wind Tunnel Measurement ◽  
Large Eddy ◽  
Vehicle Aerodynamics ◽  
Performance Computing

The world’s largest class unsteady turbulence simulations of flow around vehicles were conducted using Large Eddy Simulation (LES) on the Earth Simulator in Japan. The main objective of our study is to investigate the validity of LES, as an alternative to a conventional wind tunnel measurement or the Reynolds Averaged Navier-Stokes method, for the assessment of vehicle aerodynamics.

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

scholarly journals Containerization and wrapping of a mass spectra prediction workflow

2016 ◽  
Author(s):  
Jens Krüger ◽  
Oliver Kohlbacher
Keyword(s):  
Small Molecules ◽  
High Performance Computing ◽  
High Performance ◽  
Mass Spectra ◽  
Practical Experiences ◽  
The Individual ◽  
Performance Computing

Practical experiences are reported about implementing a workflow for the prediction of mass spectra. QCEIMS is used to simulate the fragmentation trajectories consequently leading to predicted mass spectra for small molecules, such as metabolites. The individual calculations are embedded into UNICORE workflow nodes using Docker containerization for the applications themselves. Challenges, caveats, but also advantages are discussed, providing guidance for the deployment of a scientific protocol on high performance computing resources.

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.

Sign in / Sign up

Export Citation Format

Share Document