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Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the…

Biomolecules · Quantitative Biology 2019-04-23 Kevin K. Yang , Zachary Wu , Frances H. Arnold

Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various…

Emerging Technologies · Computer Science 2022-12-23 Sasitharan Balasubramaniam , Samitha Somathilaka , Sehee Sun , Adrian Ratwatte , Massimiliano Pierobon

Multiple technologies that measure expression levels of protein mixtures in the human body offer a potential for detection and understanding the disease. The recent increase of these technologies prompts researchers to evaluate the…

Machine Learning · Computer Science 2026-05-12 Michal Valko , Richard Pelikan , Miloš Hauskrecht

Accurate and efficient characterization of nanoparticles (NPs), particularly regarding particle size distribution, is essential for advancing our understanding of their structure-property relationships and facilitating their design for…

Materials Science · Physics 2024-10-03 Arda Genc , Justin Marlowe , Anika Jalil , Libor Kovarik , Phillip Christopher

Many machine learning (ML) approaches are widely used to generate bioclimatic models for prediction of geographic range of organism as a function of climate. Applications such as prediction of range shift in organism, range of invasive…

Machine Learning · Computer Science 2013-06-19 Maumita Bhattacharya

Many machine learning (ML) approaches are widely used to generate bioclimatic models for prediction of geographic range of organism as a function of climate. Applications such as prediction of range shift in organism, range of invasive…

Machine Learning · Computer Science 2013-03-13 Maumita Bhattacharya

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…

Artificial Intelligence · Computer Science 2014-11-17 L. Leherte , J. Glasgow , K. Baxter , E. Steeg , S. Fortier

Mass spectrometry is a widely used method to study molecules and processes in medicine, life sciences, chemistry, catalysis, and industrial product quality control, among many other applications. One of the main features of some mass…

Chemical Physics · Physics 2024-07-02 Daniil A. Boiko , Valentine P. Ananikov

Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…

Biomolecules · Quantitative Biology 2021-09-29 Leonardo V. Castorina , Rokas Petrenas , Kartic Subr , Christopher W. Wood

Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…

Biomolecules · Quantitative Biology 2023-07-20 Diego E. Kleiman , Hassan Nadeem , Diwakar Shukla

Machine learning (ML) is widely used in drug discovery to train models that predict protein-ligand binding. These models are of great value to medicinal chemists, in particular if they provide case-specific insight into the physical…

Biomolecules · Quantitative Biology 2022-04-14 Carl Poelking , Gianni Chessari , Christopher W. Murray , Richard J. Hall , Lucy Colwell , Marcel Verdonk

Atomic force microscopy (AFM or SPM) imaging is one of the best matches with machine learning (ML) analysis among microscopy techniques. The digital format of AFM images allows for direct utilization in ML algorithms without the need for…

Biological Physics · Physics 2025-01-07 Igor Sokolov

Modern therapeutic antibody design often involves composing multi-part assemblages of individual functional domains, each of which may be derived from a different source or engineered independently. While these complex formats can expand…

Machine Learning · Computer Science 2025-09-25 Jiayi Xin , Aniruddh Raghu , Nick Bhattacharya , Adam Carr , Melanie Montgomery , Hunter Elliott

The tools and technology that are currently used to analyze chemical compound structures that identify polymer types in microplastics are not well-calibrated for environmentally weathered microplastics. Microplastics that have been degraded…

Machine Learning · Computer Science 2025-01-09 Sheela Ramanna , Danila Morozovskii , Sam Swanson , Jennifer Bruneau

Machine learning (ML) entered the field of computational micromagnetics only recently. The main objective of these new approaches is the automatization of solutions of parameter-dependent problems in micromagnetism such as fast response…

Computational Physics · Physics 2021-07-15 Sebastian Schaffer , Norbert J. Mauser , Thomas Schrefl , Dieter Suess , Lukas Exl

Physical and chemical conditions (kinetic temperature, volume density, molecular composition) of interstellar clouds are inherent in their mm-submm line spectra, making spectral line profiles powerful diagnostics of source conditions. We…

Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…

Computational Engineering, Finance, and Science · Computer Science 2015-10-21 Jianzhu Ma

In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…

Machine Learning · Computer Science 2021-11-04 Damiano Perri , Marco Simonetti , Andrea Lombardi , Noelia Faginas-Lago , Osvaldo Gervasi

Many important multi-component crystalline solids undergo mechanochemical spinodal decomposition: a phase transformation in which the compositional redistribution is coupled with structural changes of the crystal, resulting in dynamically…

Computational Engineering, Finance, and Science · Computer Science 2023-07-19 Xiaoxuan Zhang , Krishna Garikipati

MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…

Biomolecules · Quantitative Biology 2018-04-18 David Menéndez Hurtado , Karolis Uziela , Arne Elofsson
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