Biomolecules Papers

New Biomolecules papers from DNA, RNA, proteins, lipids. Thank you to arXiv for use of its open access interoperability.

[Earthquakes @NewEarthquake]

Revised: M5.2 → M5.6

68 km SE of Adak, Alaska
May 27 15:25 local time (6m ago)
Depth 23 km
https://t.co/OySLCZuQab

[Biomolecules Papers @Pastel]

Atom-level Protein Representation Learning Improves Protein Structure Prediction

Taewon Kim, Hyosoon Jang, Hyunjin Seo, Seonghwan Seo, Hyeongwoo Kim, Wonho Zhung, Mingyeong Shin, Wooyoun Kim, Sungsoo Ahn
https://t.co/BoZx76DZ4p [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸]

[Biomolecules Papers @Pastel]

Deep-time consistency in proteome elemental composition across cellular and viral life

L. Felipe Benites, Louie Slocombe, Sara I. Walker
https://t.co/u9mDUpjhrd [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚚-𝚋𝚒𝚘.𝙿𝙴]

[Biomolecules Papers @Pastel]

Elemental Stoichiometry as an Ecological Biosignature with Applications to Life Detection

Pilar C. Vergeli, Cole Mathis, John F. Malloy, L. Felipe Benites, Christopher P. Kempes, …
https://t.co/NUIhyVC6sD [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚊𝚜𝚝𝚛𝚘-𝚙𝚑.𝙴𝙿 𝚚-𝚋𝚒𝚘.𝙼𝙽]

[Biomolecules Papers @Pastel]

MoleCode unlocks structural intelligence in large language models

Zhiyuan Yan, Chen Liu, Boxuan Zhao, Kaiqing Lin, Jixiang Zhao, Yimi Wang, Liuzhenghao Lv, Hao Li, Shanzhuo Zhang, Li Yuan, Fanyang Mo
https://t.co/o2eHimYSR7 [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸]

[Biomolecules Papers @Pastel]

Detection of residual native state entropy changes upon mutation in Fyn SH3

Kresten Lindorff-Larsen, Robert B. Best, Anthony Mittermaier, Lewis E. Kay, Christopher M. Dobson, Michele Vendruscolo
https://t.co/Mqij7x21st [𝚚-𝚋𝚒𝚘.𝙱𝙼]

[Biomolecules Papers @Pastel]

Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction

Charles B Reilly
https://t.co/WClQYQ2Dur [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Biomolecules Papers @Pastel]

Predicting Endocrine Disruptors: A Deep Learning QSAR Model for Estrogen Receptor Activity

Belaguppa Manjunath Ashwin Desai, Shreyas Murthy, Bhoomika Sridhar, Anirudh Belaguppa Manjunath, Vivien Humtsoe, Pronama Biswas
https://t.co/yYoTfIJe0U [𝚚-𝚋𝚒𝚘.𝙱𝙼]

[Biomolecules Papers @Pastel]

Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation

Nabin Giri, Steven Farrell, Kristofer E. Bouchard
https://t.co/J9Kyi1UetE [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙰𝙸]

[Biomolecules Papers @Pastel]

TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation

Hanqun Cao, Aastha Pal, Sophia Tang, Yinuo Zhang, Jingjie Zhang, Pheng Ann Heng, Pranam Chatterjee
https://t.co/NV3LqffYPR [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

[Biomolecules Papers @Pastel]

A putative, computationally stable structure of homotrimeric BP180/collagen XVII

Congzhou M Sha
https://t.co/xKAELzAomO [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚋𝚒𝚘-𝚙𝚑 𝚙𝚑𝚢𝚜𝚒𝚌𝚜.𝚌𝚘𝚖𝚙-𝚙𝚑 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Biomolecules Papers @Pastel]

CA-DEL: An Open Multi-Target, Multi-Modal Benchmark for Learning from DNA-Encoded Library Screens

Mutian He, Hanqun Cao, Cheng Tan, Zijun Gao, Xiaojun Yao, Chunbin Gu, Pheng-Ann Heng
https://t.co/QUd6dDQ5Cp [𝚚-𝚋𝚒𝚘.𝙱𝙼]

[Biomolecules Papers @Pastel]

Enhancing Cryo-EM Density Map Segmentation in Phenix for Improved Atomic Model Building

Chenwei Zhang
https://t.co/q7q90k6haJ [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚖𝚝𝚛𝚕-𝚜𝚌𝚒 𝚌𝚜.𝙰𝙸 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Biomolecules Papers @Pastel]

Benchmarking open-source tools for in silico antiviral drug discovery

Daniel C. Elton, Preston W. Estep
https://t.co/sNahnVSQkD [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚚-𝚋𝚒𝚘.𝚀𝙼]

[Biomolecules Papers @Pastel]

AgenticPosesRanker: An Agentic AI Framework for Physically Grounded Ranking of Protein-Ligand Docking Poses

Sofiene Khiari, Amr H. Mahmoud, Markus A. Lill
https://t.co/rfFqDTu0Wh [𝚚-𝚋𝚒𝚘.𝙱𝙼]

[Biomolecules Papers @Pastel]

Complex Effects of Salt on Small-Angle X-ray Scattering of BSA Originate From the Interplay of Ions and Hydration Water

Anshika Dhiman, Sanbo Qin, Huan-Xiang Zhou
https://t.co/l8cQY241ev [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚜𝚘𝚏𝚝]

[Biomolecules Papers @Pastel]

Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics

Haocheng Tang, Liang Shi, Ya-Shi Zhang, Xixian Liu, Jian Tang, Jiarui Lu
https://t.co/E3j4Y5J9gP [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

[Biomolecules Papers @Pastel]

ConforNets: Latents-Based Conformational Control in OpenFold3

Minji Lee, Colin Kalicki, Minkyu Jeon, Aymen Qabel, Alisia Fadini, Mohammed AlQuraishi
https://t.co/l4DSmWqRpk [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]

[Biomolecules Papers @Pastel]

Boltzmann Machine Learning with a Parallel, Persistent Markov chain Monte Carlo method for Estimating Evolutionary Fields and Couplings from a Protein Multiple Sequence Alignment
https://t.co/O3fLy060SK [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚘𝚗𝚍-𝚖𝚊𝚝.𝚜𝚝𝚊𝚝-𝚖𝚎𝚌𝚑 𝚌𝚜.𝙻𝙶 𝚜𝚝𝚊𝚝.𝙼𝙻]

[Biomolecules Papers @Pastel]

PUFFIN: Protein Unit Discovery with Functional Supervision

Gökçe Uludoğan, Buse Giledereli, Elif Ozkirimli, Arzucan Özgür
https://t.co/g1bza8AU1e [𝚚-𝚋𝚒𝚘.𝙱𝙼 𝚌𝚜.𝙻𝙶]
💬to appear in ISMB 2026 proceedings