iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides

Advancing the accuracy of tyrosinase inhibitory peptides prediction via a multiview feature fusion strategy

Tyrosinase plays a crucial role as an enzyme in the production of melanin, which is the pigment accountable for determining the color of the hair, eyes, and skin. Tyrosinase inhibitory peptides (TIPs), mainly designed to regulate the activity of the enzyme tyrosinase, are of interest in various domains, including cosmetics, dermatology, and pharmaceuticals, due to their potential applications in controlling skin pigmentation. To date, a few machine learning-based models have been proposed for predicting TIPs, but their predictive performance remains unsatisfactory. In this study, we propose an innovative computational approach, named TIPred-MVFF, to accurately predict TIPs using only sequence information. Firstly, we established an up-to-date and high-quality dataset by collecting samples from various sources. Secondly, we applied a multi-view feature fusion (MVFF) strategy to extract and explore probability and category information embedded in TIPs, employing several machine learning (ML) algorithms coupled with different commonly used sequence-based feature encodings. Then, we employed resampling approaches to address the class imbalance issue. Finally, to maximize the utility of each feature, we fused probability-based and sequence-based features, generating more informative feature that were used to develop the final prediction model. Based on the independent test, experimental results showed that TIPred-MVFF outperformed several conventional ML classifiers and existing methods in terms of prediction accuracy and robustness, achieving an accuracy of 0.937 and a Matthew's correlation coefficient of 0.847. This new computational approach is anticipated to aid community-wide efforts in rapidly and cost-effectively discovering novel peptides with strong tyrosinase inhibitory activities.

AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors

MOTIVATION

Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build their own custom models. We examine different steps in the development life-cycle of peptide bioactivity binary predictors and identify key steps where automation cannot only result in a more accessible method, but also more robust and interpretable evaluation leading to more trustworthy models.

RESULTS

We present a new automated method for drawing negative peptides that achieves better balance between specificity and generalization than current alternatives. We study the effect of homology-based partitioning for generating the training and testing data subsets and demonstrate that model performance is overestimated when no such homology correction is used, which indicates that prior studies may have overestimated their performance when applied to new peptide sequences. We also conduct a systematic analysis of different protein language models as peptide representation methods and find that they can serve as better descriptors than a naive alternative, but that there is no significant difference across models with different sizes or algorithms. Finally, we demonstrate that an ensemble of optimized traditional machine learning algorithms can compete with more complex neural network models, while being more computationally efficient. We integrate these findings into AutoPeptideML, an easy-to-use AutoML tool to allow researchers without a computational background to build new predictive models for peptide bioactivity in a matter of minutes.

AVAILABILITY AND IMPLEMENTATION

Source code, documentation, and data are available at https://github.com/IBM/AutoPeptideML and a dedicated web-server at http://peptide.ucd.ie/AutoPeptideML. A static version of the software to ensure the reproduction of the results is available at https://zenodo.org/records/13363975.

Tackling the Antimicrobial Resistance "Pandemic" with Machine Learning Tools: A Summary of Available Evidence

Antimicrobial resistance is recognised as one of the top threats healthcare is bound to face in the future. There have been various attempts to preserve the efficacy of existing antimicrobials, develop new and efficient antimicrobials, manage infections with multi-drug resistant strains, and improve patient outcomes, resulting in a growing mass of routinely available data, including electronic health records and microbiological information that can be employed to develop individualised antimicrobial stewardship. Machine learning methods have been developed to predict antimicrobial resistance from whole-genome sequencing data, forecast medication susceptibility, recognise epidemic patterns for surveillance purposes, or propose new antibacterial treatments and accelerate scientific discovery. Unfortunately, there is an evident gap between the number of machine learning applications in science and the effective implementation of these systems. This narrative review highlights some of the outstanding opportunities that machine learning offers when applied in research related to antimicrobial resistance. In the future, machine learning tools may prove to be superbugs' kryptonite. This review aims to provide an overview of available publications to aid researchers that are looking to expand their work with new approaches and to acquaint them with the current application of machine learning techniques in this field.

Bioinformatics and bioactive peptides from foods: Do they work together?

We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.