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Current drug discovery is expensive and time-consuming. It remains a challenging task to create a wide variety of novel compounds with desirable pharmacological properties and cheaply available to low-income people. In this work, we develop…

Biomolecules · Quantitative Biology 2020-06-01 Kaifu Gao , Duc D Nguyen , Meihua Tu , Guo-Wei Wei

The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques of growing interest for early-stage drug discovery is de novo…

Quantitative Methods · Quantitative Biology 2020-02-18 Wenhao Gao , Connor W. Coley

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

The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

Quantitative Methods · Quantitative Biology 2025-10-03 Ekaterina Podplutova , Anastasia Vepreva , Olga A. Konovalova , Vladimir Vinogradov , Dmitrii O. Shkil , Andrei Dmitrenko

Recent advancements in large language models (LLMs) have demonstrated impressive performance in molecular generation, which offers potential to accelerate drug discovery. However, the current LLMs overlook a critical requirement for drug…

Machine Learning · Computer Science 2025-02-18 Hyosoon Jang , Yunhui Jang , Jaehyung Kim , Sungsoo Ahn

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…

Machine Learning · Computer Science 2020-07-06 Wengong Jin , Regina Barzilay , Tommi Jaakkola

Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…

Machine Learning · Computer Science 2019-06-03 Mariya Popova , Mykhailo Shvets , Junier Oliva , Olexandr Isayev

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential…

Quantitative Methods · Quantitative Biology 2025-08-27 Mahsa Sheikholeslami , Navid Mazrouei , Yousof Gheisari , Afshin Fasihi , Matin Irajpour , Ali Motahharynia

Drug development is an expensive and time-consuming process where thousands of chemical compounds are being tested in order to find those possessing drug-like properties while being safe and effective. One of key parts of the early drug…

Quantitative Methods · Quantitative Biology 2022-02-15 Josip Mesarić

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…

Machine Learning · Computer Science 2020-10-28 Bonggun Shin , Sungsoo Park , JinYeong Bak , Joyce C. Ho

De novo molecule generation often results in chemically unfeasible molecules. A natural idea to mitigate this problem is to bias the search process towards more easily synthesizable molecules using a proxy for synthetic accessibility.…

The potential number of drug like small molecules is estimated to be between 10^23 and 10^60 while current databases of known compounds are orders of magnitude smaller with approximately 10^8 compounds. This discrepancy has led to an…

Machine Learning · Computer Science 2017-05-18 Esben Jannik Bjerrum , Richard Threlfall

Drug targets are the main focus of drug discovery due to their key role in disease pathogenesis. Computational approaches are widely applied to drug development because of the increasing availability of biological molecular datasets.…

Machine Learning · Computer Science 2022-12-06 Junde Li , Collin Beaudoin , Swaroop Ghosh

In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for…

Neural and Evolutionary Computing · Computer Science 2017-01-06 Marwin H. S. Segler , Thierry Kogej , Christian Tyrchan , Mark P. Waller

A software program which aims to provide an exploration capability over the Search Space of potential drug molecules. The program explores the search space by generating random molecules, determining their fitness and then breeding a new…

Neural and Evolutionary Computing · Computer Science 2014-03-20 Mark Shackelford

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the…

Biomolecules · Quantitative Biology 2022-09-14 Kehan Wu , Yingce Xia , Yang Fan , Pan Deng , Haiguang Liu , Lijun Wu , Shufang Xie , Tong Wang , Tao Qin , Tie-Yan Liu

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial…

The development of novel pharmaceuticals represents a significant challenge in modern science, with substantial costs and time investments. Deep generative models have emerged as promising tools for accelerating drug discovery by…

Atomic Physics · Physics 2025-05-20 Adarsh Singh

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…

Biomolecules · Quantitative Biology 2023-11-17 Ayush Jain , Marie Laure-Charpignon , Irene Y. Chen , Anthony Philippakis , Ahmed Alaa

Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…

Biomolecules · Quantitative Biology 2007-11-13 Jose C Nacher , Jean-Marc Schwartz
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