The article discusses how DeepMind is speeding up the discovery of new antimicrobial peptides by employing Google Antigravity for Science. It highlights the use of this technology to accelerate the search process for novel peptides that could combat microbial threats.
OpenAI and Molecule. one show how a near-autonomous AI chemist using GPT-5.
Connor Coley works at the interface of chemistry and machine learning, to discover and design new drug compounds.
By Anne Trafton | MIT News
arXiv:2608. 11483v1 Announce Type: new Abstract: Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints.
By Kelvin P. Idanwekhai, Enes Kelestemur, Benjamin Strickland, Matthew Hart, Steini Davidsson, Angelos Angelopoulos, Ron Alterovitz, Marcello DeLuca, Alexander Tropsha
Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM agents must perceive,...
arXiv:2610.16975v1 Announce Type: new
Abstract: Drug discovery remains a resource-intensive and time-consuming process, involving billions of dollars and a decade of development to advance a drug to...
By Ye Liu, Reza Averly, Avery Meyer, Frazier N. Baker, Ruoxi Gao, Daniel Adu-Ampratwum, Xia Ning
arXiv:2608.23104v1 Announce Type: cross
Abstract: Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or we...
By Jiatong Li, Wengyu Zhang, Weida Wang, Yuxuan Ren, Wei Liu, Chenyang Mao, Yuqiang Li, Yatao Bian, Changmeng Zheng, Xiaoyong Wei, Qing Li
PepEVOLVE is a dynamic, position‑aware framework for optimizing macrocyclic peptides that learns where to edit and how to improve multiple properties. It enhances pretraining with dynamic masking and CHUCKLES shifting, employs a multi‑armed‑bandit router to identify high‑reward residues, and uses an evolving optimization algorithm with group‑relative advantage to stabilize updates. In in‑silico tests on a Rev‑binding macrocycle benchmark, PepEVOLVE surpassed PepINVENT, achieving higher permeability‑weighted scores and converging faster while respecting structural constraints.
By Trieu Nguyen, Hao-Wei Pang, Shasha Feng
arXiv:2611.07653v1 Announce Type: new
Abstract: Drug discovery requires continuous scientific decision-making across a vast research space. We introduce PharmAgents2, an autonomous system for end-to-...
By Haichuan Tan, Bowen Gao, Tao Huang, Jiaxin Tan, Xin Hong, Baoguo Yao, Yifei Wang, Zhichao Deng, Hanji Du, Dapeng Jiang, Yiheng Li, Weiwei Ma, Xin Ma, Yuqi Shi, Zixiang Wang, Kelin Wu, Tianxiang Wu, Wenxuan Xie, Jie Zang, Huiyu Zhang, Mojia Zhang, Yuying Zhang, Ya-Qin Zhang, Wei-Ying Ma, Yanyan Lan
arXiv:2607. 09998v1 Announce Type: new Abstract: Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space.
By Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
arXiv:2602. 11189v2 Announce Type: replace-cross Abstract: Modeling peptide cyclization is critical for the virtual screening of candidate peptides with desirable physical and pharmaceutical properties.
By Yitian Wang, Fanmeng Wang, Angxiao Yue, Wentao Guo, Yaning Cui, Hongteng Xu
arXiv:2603.03517v2 Announce Type: replace-cross
Abstract: General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and perfor...
By Maksim Kuznetsov, Zulfat Miftahutdinov, Rim Shayakhmetov, Mikolaj Mizera, Roman Schutski, Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev, Thomas MacDougall, Mathieu Reymond, Mihir Bafna, Kaeli Kaymak-Loveless, Eugene Babin, Maxim Malkov, Mathias Lechner, Ramin Hasani, Alexander Amini, Vladimir Aladinskiy, Alex Aliper, Alex Zhavoronkov