Neural network potentials: A concise overview of methods

E Kocer, TW Ko, J Behler - Annual review of physical chemistry, 2022 - annualreviews.org
In the past two decades, machine learning potentials (MLPs) have reached a level of
maturity that now enables applications to large-scale atomistic simulations of a wide range …

[HTML][HTML] Artificial intelligence and machine learning applications in smart production: Progress, trends, and directions

R Cioffi, M Travaglioni, G Piscitelli, A Petrillo… - Sustainability, 2020 - mdpi.com
Adaptation and innovation are extremely important to the manufacturing industry. This
development should lead to sustainable manufacturing using new technologies. To promote …

DeepBIO: an automated and interpretable deep-learning platform for high-throughput biological sequence prediction, functional annotation and visualization analysis

R Wang, Y Jiang, J Jin, C Yin, H Yu… - Nucleic acids …, 2023 - academic.oup.com
Here, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning
platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop …

Ensemble deep learning in bioinformatics

Y Cao, TA Geddes, JYH Yang, P Yang - Nature Machine Intelligence, 2020 - nature.com
The remarkable flexibility and adaptability of ensemble methods and deep learning models
have led to the proliferation of their application in bioinformatics research. Traditionally …

[HTML][HTML] Ten quick tips for machine learning in computational biology

D Chicco - BioData mining, 2017 - Springer
Abstract Machine learning has become a pivotal tool for many projects in computational
biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical …

[HTML][HTML] Materials discovery and design using machine learning

Y Liu, T Zhao, W Ju, S Shi - Journal of Materiomics, 2017 - Elsevier
The screening of novel materials with good performance and the modelling of quantitative
structure-activity relationships (QSARs), among other issues, are hot topics in the field of …

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

Z Chen, P Zhao, F Li, A Leier, TT Marquez-Lago… - …, 2018 - academic.oup.com
Structural and physiochemical descriptors extracted from sequence data have been widely
used to represent sequences and predict structural, functional, expression and interaction …

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

AS Rifaioglu, H Atas, MJ Martin… - Briefings in …, 2019 - academic.oup.com
The identification of interactions between drugs/compounds and their targets is crucial for
the development of new drugs. In vitro screening experiments (ie bioassays) are frequently …

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

Z Chen, P Zhao, C Li, F Li, D Xiang… - Nucleic acids …, 2021 - academic.oup.com
Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate
understanding of the sequence (-structure)-function paradigm for DNAs, RNAs and proteins …

Peptidomics

R Hellinger, A Sigurdsson, W Wu… - Nature Reviews …, 2023 - nature.com
Peptides are biopolymers, typically consisting of 2–50 amino acids. They are biologically
produced by the cellular ribosomal machinery or by non-ribosomal enzymes and …