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 …

Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats

CD Moon, W Young, PH Maclean… - …, 2018 - Wiley Online Library
Interests in the impact of the gastrointestinal microbiota on health and wellbeing have
extended from humans to that of companion animals. While relatively fewer studies to date …

Improving protein-ligand docking results with high-throughput molecular dynamics simulations

H Guterres, W Im - Journal of chemical information and modeling, 2020 - ACS Publications
Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …

ReaxFF molecular dynamics simulations of thermal reactivity of various fuels in pyrolysis and combustion

X Li, M Zheng, C Ren, L Guo - Energy & Fuels, 2021 - ACS Publications
The methodology development and applications of ReaxFF molecular dynamics (ReaxFF
MD) in unraveling the complex reactions and kinetics for pyrolysis and oxidation of organic …

Scaling computational genomics to millions of individuals with GPUs

A Taylor-Weiner, F Aguet, NJ Haradhvala, S Gosai… - Genome biology, 2019 - Springer
Current genomics methods are designed to handle tens to thousands of samples but will
need to scale to millions to match the pace of data and hypothesis generation in biomedical …

Oxford Nanopore sequencing: new opportunities for plant genomics?

K Dumschott, MHW Schmidt, HS Chawla… - Journal of …, 2020 - academic.oup.com
DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s,
when it was progressively supplanted by new sequencing technologies that can generate …

Electrostatic complementarity in structure-based drug design: miniperspective

BD Cons, DG Twigg, R Kumar… - Journal of medicinal …, 2022 - ACS Publications
Optimization of electrostatic complementarity is an important strategy in structure-based drug
discovery for improving the affinity of molecules against a specific protein target. In this …

Towards the interpretability of machine learning predictions for medical applications targeting personalised therapies: A cancer case survey

AJ Banegas-Luna, J Peña-García, A Iftene… - International Journal of …, 2021 - mdpi.com
Artificial Intelligence is providing astonishing results, with medicine being one of its favourite
playgrounds. Machine Learning and, in particular, Deep Neural Networks are behind this …

Mask: Redesigning the gpu memory hierarchy to support multi-application concurrency

R Ausavarungnirun, V Miller, J Landgraf… - ACM SIGPLAN …, 2018 - dl.acm.org
Graphics Processing Units (GPUs) exploit large amounts of threadlevel parallelism to
provide high instruction throughput and to efficiently hide long-latency stalls. The resulting …

Cloud computing enabled big multi-omics data analytics

S Koppad, GV Gkoutos… - … and biology insights, 2021 - journals.sagepub.com
High-throughput experiments enable researchers to explore complex multifactorial diseases
through large-scale analysis of omics data. Challenges for such high-dimensional data sets …