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  1. From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

    May 4, 2026Aritra Roy, Kevin Shen, Andrew MacBride +350Materials ScienceVast Chemical Space

  2. Bolek: A Multimodal Language Model for Molecular Reasoning

    May 4, 2026Frederic Grabowski, Jacek Szczerbiński, Maciej Jaśkowski +4Molecular Structure ElucidationMulti-Modal Large Language Models

  3. An explainable hypothesis-driven approach to Drug-Induced Liver Injury with HADES

    May 4, 2026Maciej Wisniewski, Bartosz Topolski, Pawel Dabrowski-Tumanski +2Drug-Drug InteractionsClinical Prediction

  4. MolViBench: Evaluating LLMs on Molecular Vibe Coding

    May 4, 2026Jiatong Li, Yuxuan Ren, Weida Wang +4Vast Chemical SpaceCode Generation

  5. Molecular Representations for Large Language Models

    May 3, 2026Nicholas T. Runcie, Fergus Imrie, Charlotte M. DeaneMolecular Generation

  6. Benchmarking Single-Pose Docking, Consensus Rescoring, and Supervised ML on the LIT-PCBA Library: A Critical Evaluation of DiffDock, AutoDock-GPU, GNINA, and DiffDock-NMDN

    May 3, 2026Youssef Abo-Dahab, Xiaoiang Xiang, Joanne Chun +1Structure-Based Drug DesignScreening

  7. PRIME: Protein Representation via Physics-Informed Multiscale Equivariant Hierarchies

    May 2, 2026Viet Thanh Duy Nguyen, John K. Johnstone, Truong-Son HyProtein Data BankRepresentation Learning

  8. Protein-Conditioned Multi-Objective Reinforcement Learning for Full-Length mRNA Design

    May 2, 2026Zixi Shao, Tao Wang, Yibei Xiao +1Messenger RnaProtein

  9. Knowing when to trust machine-learned interatomic potentials

    May 1, 2026Shams Mehdi, Ilkwon Cho, Olexandr IsayevInteratomic PotentialsMolecular Property Prediction

  10. Co-Generative De Novo Functional Protein Design

    May 1, 2026Xinrui Chen, Yizhen Luo, Siqi Fan +1Protein DesignFolding

  11. A Comparative Study of QSPR Methods on a Unique Multitask PAMPA dataset

    May 1, 2026Andrs Formanek, Anna Vincze, Richrd Bicsak +3Molecular Property PredictionDeep Learning

  12. Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

    May 1, 2026Fang Wu, Weihao Xuan, Heli Qi +26Protein DesignProtein

  13. VQ-SAD: Vector Quantized Structure Aware Diffusion For Molecule Generation

    May 1, 2026Farshad Noravesh, Reza Haffari, Layki Soon +1Molecular GenerationDiscrete Diffusion Model

  14. Free Energy Surface Sampling via Reduced Flow Matching

    May 1, 2026Zichen Liu, Tiejun LiFree Energy PrincipleInvertible Flows

  15. CompleteRXN: Toward Completing Open Chemical Reaction Databases

    Apr 30, 2026Gabriel Vogel, Minouk Noordsij, Evgeny Pidko +1ReactionVast Chemical Space

  16. Towards A Generative Protein Evolution Machine with DPLM-Evo

    Apr 30, 2026Xinyou Wang, Liang Hong, Jiasheng Ye +4Protein DesignEvolution

  17. Hyper-Dimensional Fingerprints as Molecular Representations

    Apr 30, 2026Jonas Teufel, Luca Torresi, André Eberhard +1Molecular OptimizationFingerprint

  18. Human-in-the-Loop Meta Bayesian Optimization for Fusion Energy and Scientific Applications

    Apr 30, 2026Ricardo Luna Gutierrez, Sahand Ghorbanpour, Ejaz Rahman +5Inertial Confinement FusionBayesian Optimization

  19. Generative structure search for efficient and diverse discovery of molecular and crystal structures

    Apr 30, 2026Yifang Qin, Yu Shi, Junfu Tan +3Crystal StructureMolecular Generation

  20. AMGenC: Generating Charge Balanced Amorphous Materials

    Apr 30, 2026Yan Lin, Jilin Hu, N. M. Anoop Krishnan +1Data-Driven Materials DiscoveryMaterials Science

  21. Do Larger Models Really Win in Drug Discovery? A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

    Apr 29, 2026Jinjiang Guo, Sheng DingDrug DiscoveryClinical Prediction

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

    Apr 28, 2026Haocheng Tang, Liang Shi, Ya-Shi Zhang +3Conformational EnsemblesMolecular Dynamics

  23. Advancing Ligand-based Virtual Screening and Molecular Generation with Pretrained Molecular Embedding Distance

    Apr 27, 2026Shiyun Wa, Yifei Wang, Simone Sciabola +1Drug DesignMolecular Generation

  24. BiMol-Diff: A Unified Diffusion Framework for Molecular Generation and Captioning

    Apr 27, 2026Aditya Hemant Shahane, Anuj Kumar Sirohi, Devansh Arora +3Molecular Generation

  25. COMO: Closed-Loop Optical Molecule Recognition with Minimum Risk Training

    Apr 26, 2026Zhuoqi Lyu, Qing KeVast Chemical SpaceMolecular Graphs

  26. CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation

    Apr 25, 2026Thibaud Southiratn, Bonil Koo, Yijingxiu Lu +1Molecular GenerationDrug Discovery

  27. Fuzzy, Neutrosophic, and Uncertain Graph Theory: Properties and Applications

    Apr 25, 2026Takaaki Fujita, Florentin SmarandacheGraph TheoryGraph Representations

  28. h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network

    Apr 25, 2026Yanru Qu, Yijie Zhang, Wenjuan Tan +6Structure-Based Drug DesignScreening

  29. HBGSA: Hydrogen Bond Graph with Self-Attention for Drug-Target Binding Affinity Prediction

    Apr 25, 2026Junxiao Kong, Chupei Tang, Di Wang +4Structure-Based Drug DesignHeterogeneous Graph Transformers

  30. C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs

    Apr 24, 2026Rui Gao, Youngseung Jeon, Swastik Roy +2Molecular OptimizationTraining-Free Reward Alignment

  31. Quotient-Space Diffusion Models

    Apr 23, 2026Yixian Xu, Yusong Wang, Shengjie Luo +4Molecular GenerationSymmetry

  32. BioMiner: A Multi-modal System for Automated Mining of Protein-Ligand Bioactivity Data from Literature

    Apr 23, 2026Jiaxian Yan, Jintao Zhu, Yuhang Yang +8Structure-Based Drug DesignLife Sciences Research

  33. Drug Synergy Prediction via Residual Graph Isomorphism Networks and Attention Mechanisms

    Apr 23, 2026Jiyan Song, Wenyang Wang, Chengcheng Yan +2Drug-Drug InteractionsSynergy

  34. Mol-Debate: Multi-Agent Debate Improves Structural Reasoning in Molecular Design

    Apr 22, 2026Wengyu Zhang, Xiao-Yong Wei, Qing LiDrug DesignDrug Discovery

  35. Multi-Objective Reinforcement Learning for Generating Covalent Inhibitor Candidates

    Apr 21, 2026Renee GilDrug Design

  36. Structure-guided molecular design with contrastive 3D protein-ligand learning

    Apr 21, 2026Carles Navarro, Philipp Tholke, Gianni de FabritiisStructure-Based Drug DesignVast Chemical Space

  37. Multimodal Transformer for Sample-Aware Prediction of Metal-Organic Framework Properties

    Apr 21, 2026Seunghee Han, Jaewoong Lee, Jihan KimMolecular Property PredictionCryo-Electron Microscopy

  38. When Active Learning Falls Short: An Empirical Study on Chemical Reaction Extraction

    Apr 21, 2026Simin Yu, Sufia FathimaReactionActive Learning

  39. Graph-Theoretic Models for the Prediction of Molecular Measurements

    Apr 21, 2026Anna Niane, Prudence DjagbaMolecular Property PredictionMolecular Structure Elucidation

  40. ConforNets: Latents-Based Conformational Control in OpenFold3

    Apr 20, 2026Minji Lee, Colin Kalicki, Minkyu Jeon +3Conformational EnsemblesMixformer

  41. An Integrated Deep-Learning Framework for Peptide-Protein Interaction Prediction and Target-Conditioned Peptide Generation with ConGA-PepPI and TC-PepGen

    Apr 20, 2026Chupei Tang, Junxiao Kong, Moyu Tang +5Cyclic PeptidesProtein

  42. Predictive Modelling of Natural Medicinal Compounds for Alzheimer disease Using Machine Learning and Cheminformatics

    Apr 20, 2026Hafiza Syeda Yusra Tirmizi, Syed Ibad Hasnain, Muhammad Faris +2Molecular Property PredictionAlzheimer

  43. How Creative Are Large Language Models in Generating Molecules?

    Apr 20, 2026Wen Tao, Yiwei Wang, Peng Zhou +6Molecular GenerationCreativity

  44. Boltzmann Machine Learning with a Parallel, Persistent Markov chain Monte Carlo method for Estimating Evolutionary Fields and Couplings from a Protein Multiple Sequence Alignment

    Apr 20, 2026Sanzo MiyazawaProtein Data BankMarkov Chain Monte Carlo

  45. Prior-Fitted Functional Flow: In-Context Generative Models for Pharmacokinetics

    Apr 19, 2026César Ojeda, Niklas Hartung, Wilhelm Huisinga +6Drug-Drug InteractionsPatient Trajectories

  46. RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

    Apr 19, 2026Meghana Kshirsagar, Allen Nie, Ching-An Cheng +5Protein DesignSequence Modeling

  47. ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design

    Apr 18, 2026Yutang Ge, Guojiang Zhao, Sihang Li +7Protein DesignFolding

  48. KinetiDiff: Docking-Guided Diffusion for De Novo ACVR1 Inhibitor Design in Fibrodysplasia Ossificans Progressiva

    Apr 17, 2026Aaryan PatelDrug DesignCervical Spine

  49. FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

    Apr 17, 2026Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar +4Tandem Mass SpectraMolecular Generation

  50. Evaluating the Progression of Large Language Model Capabilities for Small-Molecule Drug Design

    Apr 17, 2026Shriram Chennakesavalu, Kirill Shmilovich, Hayley Weir +5Drug Design

  51. Large Language Models Meet Biomedical Knowledge Graphs for Mechanistically Grounded Therapeutic Prioritization

    Apr 17, 2026Chih-Hsuan Wei, Chi-Ping Day, Zhizheng Wang +8Biomedical Knowledge GraphDrug Discovery

  52. A Systematic Survey and Benchmark of Deep Learning for Molecular Property Prediction in the Foundation Model Era

    Apr 17, 2026Zongru Li, Xingsheng Chen, Honggang Wen +8Molecular Property PredictionComputational Chemistry

  53. Tabular foundation models for in-context prediction of molecular properties

    Apr 17, 2026Karim K. Ben Hicham, Jan G. Rittig, Martin Grohe +1Molecular Property PredictionTabular Foundation Models

  54. ReactBench: A Benchmark for Topological Reasoning in MLLMs on Chemical Reaction Diagrams

    Apr 17, 2026Qiang Xu, Shengyuan Bai, Yu Wang +6Reasoning BenchmarkVisual Reasoning

  55. An Interpretable Framework Applying Protein Words to Predict Protein-Small Molecule Complementary Pairing Rules

    Apr 17, 2026Jingke Chen, Jingrui Zhong, Tazneen Hossain Tani +3Structure-Based Drug DesignModel Interpretability

  56. Reward Weighted Classifier-Free Guidance as Policy Improvement in Autoregressive Models

    Apr 16, 2026Alexander Peysakhovich, William BermanExternal Reward ModelsAutoregressive Model

  57. Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

    Apr 16, 2026Mariia Ivonina, Jakub RydzewskiMessenger RnaConformational Ensembles

  58. PUFFIN: Protein Unit Discovery with Functional Supervision

    Apr 16, 2026Gökçe Uludoğan, Buse Giledereli, Elif Ozkirimli +1Protein Data BankProtein

  59. Finetuning-Free Diffusion Model with Adaptive Constraint Guidance for Inorganic Crystal Structure Generation

    Apr 14, 2026Auguste de Lambilly, Vladimir Baturin, David Portehault +4Crystal StructureCrystal

  60. LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization

    Apr 9, 2026Tao Li, Kaiyuan Hou, Tuan Vinh +4Molecular OptimizationReaction