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Related papers: AI-guided Antibiotic Discovery Pipeline from Targe…

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Antibiotic resistance is a growing public health problem. To gain a fundamental understanding of resistance evolution, a combination of systematic experimental and theoretical approaches is required. Evolution experiments combined with…

Populations and Evolution · Quantitative Biology 2021-05-24 Gabriela Petrungaro , Yuval Mulla , Tobias Bollenbach

Antimicrobial resistance is an emerging global health crisis that is undermining advances in modern medicine and, if unmitigated, threatens to kill 10 million people per year worldwide by 2050. Research over the last decade has demonstrated…

Quantitative Methods · Quantitative Biology 2020-09-24 K. Farquhar , H. Flohr , D. A. Charlebois

The disconnect between AI-generated molecules with desirable properties and their synthetic feasibility remains a critical bottleneck in computational discovery of drugs and materials. While generative AI has accelerated the proposal of…

Chemical Physics · Physics 2025-11-25 Shuan Chen , Gunwook Nam , Alan Aspuru-Guzik , Yousung Jung

Antimicrobial Resistance (AMR) is a rapidly escalating global health crisis. While genomic sequencing enables rapid prediction of resistance phenotypes, current computational methods have limitations. Standard machine learning models treat…

Machine Learning · Computer Science 2025-09-30 Md. Saiful Bari Siddiqui , Nowshin Tarannum

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

Antibodies, a prominent class of approved biologics, play a crucial role in detecting foreign antigens. The effectiveness of antigen neutralisation and elimination hinges upon the strength, sensitivity, and specificity of the…

Quantitative Methods · Quantitative Biology 2023-09-06 Bruna Moreira da Silva , David B. Ascher , Nicholas Geard , Douglas E. V. Pires

Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of…

Antibodies are essential proteins responsible for immune responses in organisms, capable of specifically recognizing antigen molecules of pathogens. Recent advances in generative models have significantly enhanced rational antibody design.…

Artificial Intelligence · Computer Science 2025-11-10 Zichen Wang , Yaokun Ji , Jianing Tian , Shuangjia Zheng

Drug discovery remains a slow and expensive process that involves many steps, from detecting the target structure to obtaining approval from the Food and Drug Administration (FDA), and is often riddled with safety concerns. Accurate…

Quantitative Methods · Quantitative Biology 2025-08-22 Ali Vefghi , Zahed Rahmati , Mohammad Akbari

Antimicrobial resistance is one of the biggest health problem, especially in the current period of COVID-19 pandemic. Due to the unique membrane-destruction bactericidal mechanism, antimicrobial peptide-mimetic copolymers are paid more…

Biomolecules · Quantitative Biology 2022-12-09 Tianyu Wu , Yang Tang

The evolution of antibiotic resistance among bacteria threatens our continued ability to treat infectious diseases. The need for sustainable strategies to cure bacterial infections has never been greater. So far, all attempts to restore…

Populations and Evolution · Quantitative Biology 2015-06-12 Christiane P. Goulart , Mentar Mahmudi , Kristina A. Crona , Stephen D. Jacobs , Marcelo Kallmann , Barry G. Hall , Devin C. Greene , Miriam Barlow

The rapid advancement of artificial intelligence, particularly autonomous agentic systems based on Large Language Models (LLMs), presents new opportunities to accelerate drug discovery by improving in-silico modeling and reducing dependence…

Recently, deep learning has made rapid progress in antibody design, which plays a key role in the advancement of therapeutics. A dominant paradigm is to train a model to jointly generate the antibody sequence and the structure as a…

Quantitative Methods · Quantitative Biology 2025-01-20 Nayoung Kim , Minsu Kim , Sungsoo Ahn , Jinkyoo Park

The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original…

Biomolecules · Quantitative Biology 2021-02-08 Yuemin Bian , Xiang-Qun Xie

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…

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

Antibody therapeutics has been extensively studied in drug discovery and development within the past decades. One increasingly popular focus in the antibody discovery pipeline is the optimization step for therapeutic leads. Both traditional…

Biomolecules · Quantitative Biology 2022-08-16 Yue Kang , Dawei Leng , Jinjiang Guo , Lurong Pan

Predicting the binding free energy between antibodies and antigens is a key challenge in structure-aware biomolecular modeling, with direct implications for antibody design. Most existing methods either rely solely on sequence embeddings or…

Biomolecules · Quantitative Biology 2025-08-28 Ciyuan Yu , Hongzong Li , Jiahao Ma , Shiqin Tang , Ye-Fan Hu , Jian-Dong Huang

Research around AI for Science has seen significant success since the rise of deep learning models over the past decade, even with longstanding challenges such as protein structure prediction. However, this fast development inevitably made…

Artificial Intelligence · Computer Science 2022-12-27 Kieran Didi , Matej Zečević

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the…

Biomolecules · Quantitative Biology 2024-06-27 Xiangru Tang , Howard Dai , Elizabeth Knight , Fang Wu , Yunyang Li , Tianxiao Li , Mark Gerstein