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New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug, takes decades. Although progress in molecular property prediction using machine-learning…

Accelerating the discovery of structural materials is essential for applications in hard and refractory alloys, hypersonic platforms, nuclear systems, and other extreme environment technologies. Progress is often constrained by slow…

Materials Science · Physics 2025-12-16 Vivek Chawla , Dayakar Penumadu , Sergei Kalinin

In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…

Quantitative Methods · Quantitative Biology 2018-07-03 Weijun Zhu

DNA-binding proteins are a class of proteins which have a specific or general affinity to DNA and include three important components: transcription factors; nucleases, and histones. DNA-binding proteins also perform important roles in many…

Computer Vision and Pattern Recognition · Computer Science 2012-07-12 Sokyna Qatawneh , Afaf Alneaimi , Thamer Rawashdeh , Mmohammad Muhairat , Rami Qahwaji , Stan Ipson

In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank…

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

Domain-aware machine learning (ML) models have been increasingly adopted for accelerating small molecule therapeutic design in the recent years. These models have been enabled by significant advancement in state-of-the-art artificial…

Machine Learning · Computer Science 2021-02-12 Rajendra P. Joshi , Neeraj Kumar

In recent years, object detection in deep learning has experienced rapid development. However, most existing object detection models perform well only on closed-set datasets, ignoring a large number of potential objects whose categories are…

Computer Vision and Pattern Recognition · Computer Science 2024-03-01 Juexiao Feng , Yuhong Yang , Yanchun Xie , Yaqian Li , Yandong Guo , Yuchen Guo , Yuwei He , Liuyu Xiang , Guiguang Ding

In recent years the machine learning techniques have shown a great potential in various problems from a multitude of disciplines, including materials design and drug discovery. The high computational speed on the one hand and the accuracy…

Chemical Physics · Physics 2018-05-09 Konstantin Gubaev , Evgeny V. Podryabinkin , Alexander V. Shapeev

Drug discovery using deep learning has attracted a lot of attention of late as it has obvious advantages like higher efficiency, less manual guessing and faster process time. In this paper, we present a novel neural network for generating…

Biomolecules · Quantitative Biology 2021-10-08 Abhinav Sagar

Identifying protein targets for small molecules, or reverse screening, is essential for understanding drug action, guiding compound repurposing, predicting off-target effects, and elucidating the molecular mechanisms of bioactive compounds.…

Biomolecules · Quantitative Biology 2026-01-21 Shengjie Xu , Xianbin Ye , Mengran Zhu , Xiaonan Zhang , Shanzhuo Zhang , Xiaomin Fang

Due to their excellent drug-like and pharmacokinetic properties, small molecule drugs are widely used to treat various diseases, making them a critical component of drug discovery. In recent years, with the rapid development of deep…

Machine Learning · Computer Science 2025-05-15 Kun Li , Yida Xiong , Hongzhi Zhang , Xiantao Cai , Jia Wu , Bo Du , Wenbin Hu

For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state of the…

Machine Learning (ML) and Deep Learning (DL) have been used for building Intrusion Detection Systems (IDS). The increase in both the number and sheer variety of new cyber-attacks poses a tremendous challenge for IDS solutions that rely on a…

Cryptography and Security · Computer Science 2020-11-17 Hanan Hindy , Robert Atkinson , Christos Tachtatzis , Jean-Noël Colin , Ethan Bayne , Xavier Bellekens

The identification of protein-ligand interaction plays a key role in biochemical research and drug discovery. Although deep learning has recently shown great promise in discovering new drugs, there remains a gap between deep learning-based…

Molecular Networks · Quantitative Biology 2021-08-10 Fan Hu , Lei Wang , Yishen Hu , Dongqi Wang , Weijie Wang , Jianbing Jiang , Nan Li , Peng Yin

Digital systems find it challenging to keep up with cybersecurity threats. The daily emergence of more than 560,000 new malware strains poses significant hazards to the digital ecosystem. The traditional malware detection methods fail to…

Cryptography and Security · Computer Science 2025-04-28 Abrar Fahim , Shamik Dey , Md. Nurul Absur , Md Kamrul Siam , Md. Tahmidul Huque , Jafreen Jafor Godhuli

Controlling infectious diseases is a major health priority because they can spread and infect humans, thus evolving into epidemics or pandemics. Therefore, early detection of infectious diseases is a significant need, and many researchers…

Machine Learning · Computer Science 2022-06-16 Eman Yahia Alqaissi , Fahd Saleh Alotaibi , Muhammad Sher Ramzan

In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop…

Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of…

Biomolecules · Quantitative Biology 2024-07-30 Nikolai Schapin , Carles Navarro , Albert Bou , Gianni De Fabritiis

Few-shot learning is a promising approach to molecular property prediction as supervised data is often very limited. However, many important molecular properties depend on complex molecular characteristics -- such as the various 3D…

Machine Learning · Computer Science 2023-10-10 Christopher Fifty , Joseph M. Paggi , Ehsan Amid , Jure Leskovec , Ron Dror

To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow.…

Biomolecules · Quantitative Biology 2020-01-07 Zachary Wu , S. B. Jennifer Kan , Russell D. Lewis , Bruce J. Wittmann , Frances H. Arnold