[HTML][HTML] A structure-based drug discovery paradigm
Structure-based drug design is becoming an essential tool for faster and more cost-efficient
lead discovery relative to the traditional method. Genomic, proteomic, and structural studies …
lead discovery relative to the traditional method. Genomic, proteomic, and structural studies …
[HTML][HTML] Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview
V Salmaso, S Moro - Frontiers in pharmacology, 2018 - frontiersin.org
Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …
1980s. Given the low computational resources of the time, the first molecular modeling …
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design
C Kutzner, C Kniep, A Cherian… - Journal of Chemical …, 2022 - ACS Publications
We assess costs and efficiency of state-of-the-art high-performance cloud computing and
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
compare the results to traditional on-premises compute clusters. Our use case is atomistic …
Making it rain: cloud-based molecular simulations for everyone
PR Arantes, MD Polêto, C Pedebos… - Journal of Chemical …, 2021 - ACS Publications
We present a user-friendly front-end for running molecular dynamics (MD) simulations using
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
the OpenMM toolkit on the Google Colab framework. Our goals are (1) to highlight the usage …
Finding the hidden path: Time bounds for all-pairs shortest paths
The all-pairs shortest-paths problem in weighted graphs is investigated. An algorithm—the
Hidden-Paths Algorithm—that finds these paths in time O(m^*n+n^2\logn), where m^* is the …
Hidden-Paths Algorithm—that finds these paths in time O(m^*n+n^2\logn), where m^* is the …
Cloud computing in healthcare and biomedicine
B Calabrese, M Cannataro - Scalable Computing: Practice and Experience, 2015 - scpe.org
High throughput platforms available in clinical settings or in research laboratories, such as
magnetic resonance imaging, microarray, mass spectrometry and next-generation …
magnetic resonance imaging, microarray, mass spectrometry and next-generation …
A survey of biological data in a big data perspective
The amount of available data is continuously growing. This phenomenon promotes a new
concept, named big data. The highlight technologies related to big data are cloud computing …
concept, named big data. The highlight technologies related to big data are cloud computing …
Applying high-performance computing in drug discovery and molecular simulation
T Liu, D Lu, H Zhang, M Zheng, H Yang… - National science …, 2016 - academic.oup.com
In recent decades, high-performance computing (HPC) technologies and supercomputers in
China have significantly advanced, resulting in remarkable achievements. Computational …
China have significantly advanced, resulting in remarkable achievements. Computational …
[HTML][HTML] Putative histidine kinase inhibitors with antibacterial effect against multi-drug resistant clinical isolates identified by in vitro and in silico screens
Novel antibacterials are urgently needed to address the growing problem of bacterial
resistance to conventional antibiotics. Two-component systems (TCS) are widely used by …
resistance to conventional antibiotics. Two-component systems (TCS) are widely used by …
[HTML][HTML] Comprehensive survey of consensus docking for high-throughput virtual screening
C Blanes-Mira, P Fernández-Aguado… - Molecules, 2022 - mdpi.com
The rapid advances of 3D techniques for the structural determination of proteins and the
development of numerous computational methods and strategies have led to identifying …
development of numerous computational methods and strategies have led to identifying …