AgentFold is a multi‑agent framework that treats protein‑folding model design as a closed‑loop search over executable code variants. Starting from the ESMFold codebase, the agents generate hypotheses, modify and debug code, evaluate model variants, and store both successes and failures in structured memory, guided by an MCTS‑style policy that allocates GPU resources. In an engineering‑scale experiment, AgentFold explored about 80 variants using 5,000 GPU‑hours and 170 million LLM tokens, improving the best lDDT score by 7.5% over independent Codex proposals and outperforming a random‑search baseline, while also uncovering empirical design patterns such as the benefits of early, soft, learnable priors.
By Mingquan Liu, Jiangyu Chen, Hanqun Cao, Xujun Zhang, Pengsen Ma, Xiangru Tang, Shuting Jin, Zhuo Yang, Tianfan Fu, Fang Wu, Xiangxiang Zeng
arXiv:2609.05818v1 Announce Type: new
Abstract: We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use...
By Bryce Cai, Geetha Jeyapragasan, Samira Nedungadi, Jake Yukich, Seth Donoughe
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: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
arXiv:2608. 06961v1 Announce Type: new Abstract: Early-stage molecular design is an iterative process, not just a task of generating molecules.
By Zhu Wang, Jiangyu Chen, Yingjun Shang, Yuhui Yao, Laiao Lu, Tianfan Fu, Na Zou
arXiv:2606. 31229v1 Announce Type: new Abstract: Ideation plays a pivotal role in scientific discovery.
By Keyu Zhao, Lingyan Kong, Fengli Xu, Yong Li
El Agente Potente is an agentic system that integrates typed execution graphs and a coding mode to facilitate machine‑learning interatomic potential (MLIP) driven atomistic simulations. Typed execution graphs offer structured, provenance‑aware workflows where large language models handle planning and routing while deterministic Python code performs scientific computation and validation. The coding agent builds customized workflows for tasks needing procedural flexibility, invoking existing Potente functions for supported calculations. The system is demonstrated across materials discovery, energy‑landscape exploration, adsorption, and catalytic reaction workflows, with benchmarks on reproducibility and LLM token cost.
By Tsz Wai Ko, Jiaru Bai, Thomas Swanick, Yeonghun Kang, Changhyeok Choi, Angelina Qihong Jiang, Aiwei Yin, Varinia Bernales, Al\'an Aspuru-Guzik
arXiv:2607. 08403v1 Announce Type: new Abstract: The application of lightweight Large Language Models in rule-based scientific domains remains severely limited by their tendency to mimic linguistic patterns rather than reproduce axiomatic reasoning, causing frequent hallucinations.
By Runzhe Liu, Biquan Bie, Zihao Wang, Yuchao Ma, Yexin Liu, Xinghai Li, Harry Yang, Wenbo Yang, Jinzhe Cao, Shengyang Tao
MolDesignBench is a new benchmark for evaluating large language model (LLM)-based agents in scenario‑grounded molecular design. It contains 2,000 generation and optimization tasks that blend implicit narrative requirements with explicit property and functional‑group constraints, including infeasible cases, and require the use of 17 specialized chemistry tools. Experiments with leading LLMs show low success rates (best ~43%) and highlight failures in implicit‑constraint reasoning, infeasibility detection, and tool usage, underscoring the benchmark’s role in identifying key bottlenecks for future research.
By Yongjun Jeong, Hanbum Ko, Ye Rin Kim, Chanhui Lee, Rodrigo Hormazabal, Jaewan Lee, Sehui Han, Sungbin Lim, Sungwoong Kim
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.
By C\'esar Ojeda, Darius A. Faroughy, Maryam Karimi, Payam Zarrintaj, Mir Mehdi Seyedebrahimi, Mart\'in Carballo-Pacheco
The paper introduces MADA, a Large Language Model–powered multi‑agent framework that coordinates specialized agents—Job Management, Geometry, and Inverse Design—to automate complex design workflows on high‑performance computing systems. In the context of Richtmyer–Meshkov Instability suppression for Inertial Confinement Fusion, MADA iteratively refines designs by launching ensemble simulations, generating meshes, and proposing new designs based on simulation outcomes, achieving improved suppression with minimal manual effort. The framework demonstrates how coordinated reasoning, simulation, and specialized tools can be scaled for rapid, automated design exploration.
By Harshitha Menon, Charles F. Jekel, Kevin Korner, M. Giselle Fernandez-Godino, Brian Gunnarson, Nathan K. Brown, Michael Stees, Walter Nissen, Meir H. Shachar, Dane M. Sterbentz, William J. Schill, Yue Hao, Robert Rieben, William Quadros, Steve Owen, Scott Mitchell, Ismael D. Boureima, Jonathan L. Belof
arXiv:2606. 12916v1 Announce Type: new Abstract: Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics.
By Zehong Wang, Yijun Ma, Connor R. Schmidt, Tianyi Ma, Weixiang Sun, Ziming Li, Xiaoguang Guo, Chuxu Zhang, Matthew J. Webber, Yanfang Ye