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In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to…

In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…

Quantitative Methods · Quantitative Biology 2024-02-26 Yifan Wu , Yousong Peng

Magnetic nanoparticles offer unique potential for various technological, biomedical, or environmental applications thanks to the size-, shape- and material-dependent tunability of their magnetic properties. To optimize particles for a…

There remains an urgent need to identify existing drugs that might be suitable for treating patients suffering from COVID-19 infection. Drugs rarely act at a single molecular target, with off target effects often being responsible for…

Biomolecules · Quantitative Biology 2020-09-03 Sakshi Piplani , Puneet Singh , Nikolai Petrovsky , David A. Winkler

The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…

Soft Condensed Matter · Physics 2019-08-23 Suman Saurabh , Francesco Piazza

Traditional drug discovery is a long, expensive, and complex process. Advances in Artificial Intelligence (AI) and Machine Learning (ML) are beginning to change this narrative. Here, we provide a comprehensive overview of different AI and…

Artificial Intelligence · Computer Science 2024-11-12 Khartik Uppalapati , Eeshan Dandamudi , S. Nick Ice , Gaurav Chandra , Kirsten Bischof , Christian L. Lorson , Kamal Singh

The vibrational behavior of molecules serves as a crucial fingerprint of their structure, chemical state, and surrounding environment. Neutron vibrational spectroscopy provides comprehensive measurements of vibrational modes without…

Chemical Physics · Physics 2025-02-19 Bowen Han , Pei Zhang , Kshitij Mehta , Massimiliano Lupo Pasini , Mingda Li , Yongqiang Cheng

The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing…

Quantitative Methods · Quantitative Biology 2024-09-10 Yizhen Zheng , Huan Yee Koh , Maddie Yang , Li Li , Lauren T. May , Geoffrey I. Webb , Shirui Pan , George Church

Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible chemical space. Together, these approaches have the…

Biomolecules · Quantitative Biology 2025-10-15 Shanzhuo Zhang , Xianbin Ye , Donglong He , Yueyang Huang , Xiaonan Zhang , Xiaomin Fang

Nuclear magnetic resonance (NMR) schemes can be applied to micron-, and nanometer-sized samples by the aid of quantum sensors such as nitrogen-vacancy (NV) color centers in diamond. These minute devices allow for magnetometry of nuclear…

Quantum Physics · Physics 2021-07-19 C. Munuera-Javaloy , R. Puebla , J. Casanova

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more…

Biomolecules · Quantitative Biology 2018-08-14 Erick Martins Ratamero , Dom Bellini , Christopher G. Dowson , Rudolf A. Roemer

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

Machine Learning · Computer Science 2020-02-10 Paul Maragakis , Hunter Nisonoff , Brian Cole , David E. Shaw

For over three decades, scanning probe microscopy (SPM) has been a key method for exploring material structures and functionalities at nanometer and often atomic scales in ambient, liquid, and vacuum environments. Historically, SPM…

Accurate MR signal simulation, including microvascular structures and water diffusion, is crucial for MRI techniques like fMRI BOLD modeling and MR vascular Fingerprinting (MRF), which use susceptibility effects on MR signals for tissue…

In this paper, we address the problem of real-time detection of viruses docking to nanowires, especially when multiple viruses dock to the same nano-wire. The task becomes more complicated when there is an array of nanowires coated with…

Artificial Intelligence · Computer Science 2014-07-18 Shalini Ghosh , Patrick Lincoln , Christian Petersen , Alfonso Valdes

Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of…

Biomolecules · Quantitative Biology 2023-08-25 Nikolai Schapin , Maciej Majewski , Alejandro Varela , Carlos Arroniz , Gianni De Fabritiis

Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) are versatile tools with broad applications from physics and chemistry to geology and medical studies. In this mini-review, we consider the concepts of NMR and MRI…

Medical Physics · Physics 2024-01-04 Fatemeh Khashami

The article proposes a conceptual approach for evaluating the impact of engineered nanoparticles (NPs) on the functionality of small biomolecules. The developed machine learning (ML) model is based on in-silico 13C NMR spectroscopy chemical…

Other Quantitative Biology · Quantitative Biology 2026-03-23 Mariya L Ivanova , Michael Nichols , Nicola Russo , Gueorgui Mihaylov , Konstantin Nikolic

The COVID-19 pandemic has presented many challenges that have spurred biotechnological research to address specific problems. Diagnostics is one area where biotechnology has been critical. Diagnostic tests play a vital role in managing a…

Optically-probed nitrogen-vacancy (NV) quantum defects in diamond can detect nuclear magnetic resonance (NMR) signals with high-spectral resolution from micron-scale sample volumes of about 10 picoliters. However, a key challenge for NV-NMR…