Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints | Paper Citation Record

Observation 0007c43a-5b88-430c-9272-95a23471b9bb · outbound

This paper cites Pocket2Mol: Efficient molecular sampling based on 3D protein pockets.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Pocket2Mol: Efficient molecular sampling based on 3D protein pockets

Reference 1

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Observation 8881c6ca-eb0b-42ce-b79e-d36fb1ae8eab · outbound

This paper cites 3D equivariant diffusion for target-aware molecule generation and affinity prediction.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints 3D equivariant diffusion for target-aware molecule generation and affinity prediction

Reference 2

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Observation df3ed84e-3db6-4330-9f44-89cae312828a · outbound

This paper cites Blundell, Pietro Lio, Max Welling, Michael Bronstein, and Bruno Correia.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Blundell, Pietro Lio, Max Welling, Michael Bronstein, and Bruno Correia

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:06.339475Z

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Observation bedb7919-2ba1-4602-a198-0d39e8314ceb · outbound

This paper cites A dual diffusion model enables 3d molecule generation and lead optimization based on target pockets.Nature Communications, 15(1):2657, Mar 2024.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints A dual diffusion model enables 3d molecule generation and lead optimization based on target pockets.Nature Communications, 15(1):2657, Mar 2024

Reference 4

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Observation eabcab87-e180-4d3e-8428-5d19f6b0b896 · outbound

This paper cites Aligning target-aware molecule diffusion models with exact energy optimization.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Aligning target-aware molecule diffusion models with exact energy optimization

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:06.522472Z

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Observation e41722be-228a-4279-abb4-769512d9976e · outbound

This paper cites SGEDiff: a subgraph-enriched diffusion model for structure-based 3d molecular generation.Journal of Cheminformatics, 17(1):175, Dec 2025.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints SGEDiff: a subgraph-enriched diffusion model for structure-based 3d molecular generation.Journal of Cheminformatics, 17(1):175, Dec 2025

Reference 6

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.945355Z

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Observation 1270cfb6-a9cb-451f-929d-de8fada84825 · outbound

This paper cites Steering semi-flexible molecular diffusion model for structure-based drug design with reinforcement learning.Science Advances, 12(16):eady9955, 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Steering semi-flexible molecular diffusion model for structure-based drug design with reinforcement learning.Science Advances, 12(16):eady9955, 2026

Reference 7

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Observation f9af9fca-0493-401f-aaaa-fb0633505e07 · outbound

This paper cites DiffDec: Structure-aware scaffold decoration with an end-to-end diffusion model.Journal of Chemical Information and Modeling, 64(7):2554–2564, 2024.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints DiffDec: Structure-aware scaffold decoration with an end-to-end diffusion model.Journal of Chemical Information and Modeling, 64(7):2554–2564, 2024

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:06.785877Z

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Observation 98462f00-c5a8-4b38-b80e-2e586acd461c · outbound

This paper cites Protein-ligand interaction prior for binding- aware 3d molecule diffusion models.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Protein-ligand interaction prior for binding- aware 3d molecule diffusion models

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:06.911505Z

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Observation 0fb09f76-7935-4986-87cc-d4abc308bcb2 · outbound

This paper cites an unresolved cited work.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

Reference 10

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Observation 1bd725c1-79cd-49ab-904c-f242fb874543 · outbound

This paper cites Interaction-constrained 3d molec- ular generation using a diffusion model enables structure-based pharmacophore model- ing for drug design.npj Drug Discovery, 3(1):8, Mar 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Interaction-constrained 3d molec- ular generation using a diffusion model enables structure-based pharmacophore model- ing for drug design.npj Drug Discovery, 3(1):8, Mar 2026

Reference 11

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.659913Z

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Observation 16150835-d0f1-42c4-a946-4ed2414876c6 · outbound

This paper cites Cassady, Michael A.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Cassady, Michael A

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:07.238170Z

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Observation bb719584-9bd3-4196-bdfa-cc9bae6cf255 · outbound

This paper cites Conversational drug editing using retrieval and domain feedback.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Conversational drug editing using retrieval and domain feedback

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:07.319746Z

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Observation 597e9dfd-8066-44be-8ada-df609dee3a78 · outbound

This paper cites Baker, Ziqi Chen, Xia Ning, and Huan Sun.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Baker, Ziqi Chen, Xia Ning, and Huan Sun

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:07.472299Z

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Observation 4ea5aed6-d79e-46e4-bdac-02cbe47cc560 · outbound

This paper cites Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files,.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files,

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:07.596565Z

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Observation 94d794b6-a126-4741-89b4-ee835a50f18f · outbound

This paper cites an unresolved cited work.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

Reference 16

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.510261Z

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Observation 5e1aa066-97df-4e95-a089-5cfcfe1ccd1a · outbound

This paper cites nach0-pc: Multi-task language model with molecular point cloud encoder.Proceedings of the AAAI Conference on Artificial Intelligence, 39(23): 24357–24365, Apr.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints nach0-pc: Multi-task language model with molecular point cloud encoder.Proceedings of the AAAI Conference on Artificial Intelligence, 39(23): 24357–24365, Apr

Reference 17

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.366980Z

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Observation d416ccfa-d2d6-4f0c-8ff1-df6ec63092ce · outbound

This paper cites Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B

Reference 18

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.232790Z

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Observation afd50b71-6bfe-40ed-94c6-1704d42a8fee · outbound

This paper cites PLINDER: The protein-ligand interactions dataset and resource.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints PLINDER: The protein-ligand interactions dataset and resource

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:08.158376Z

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Observation e1b2db8f-a815-458a-bccf-c12d5f9944d1 · outbound

This paper cites The PDBbind database: Methodologies and updates.Journal of Medicinal Chemistry, 48(12):4111–4119,.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints The PDBbind database: Methodologies and updates.Journal of Medicinal Chemistry, 48(12):4111–4119,

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:08.271280Z

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Observation 35d96ff3-4609-4061-a62f-d9152d6e6dc5 · outbound

This paper cites Smith, Anthony J.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Smith, Anthony J

Reference 21

Resolution: verified exact; doi, observed 2026-08-01T15:58:32.052214Z

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Observation e400f038-607a-46f7-8407-ee7fc0114069 · outbound

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

Reference 22

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Observation fa6dfa14-e5fb-4477-9442-9ae9d8bdf641 · outbound

This paper cites an unresolved cited work.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

Reference 23

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Observation c309474b-7ba5-4de9-af86-5785ad3a8f77 · outbound

This paper cites Durian: A comprehensive benchmark for structure-based 3d molecular generation.Journal of Chemical Information and Modeling, 65(1):173–186, 2025.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Durian: A comprehensive benchmark for structure-based 3d molecular generation.Journal of Chemical Information and Modeling, 65(1):173–186, 2025

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.762246Z

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Observation b6826d9f-87d1-492a-b0e8-afd3136e275f · outbound

This paper cites MolDiff: Addressing the atom- bond inconsistency problem in 3D molecule diffusion generation.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints MolDiff: Addressing the atom- bond inconsistency problem in 3D molecule diffusion generation

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Observation 21663e6a-d1c8-4834-be55-3f0ef8e3dbdb · outbound

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

Reference 26

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Observation a776d0ce-9de3-4c8d-a520-d64304754e70 · outbound

This paper cites Binding-adaptive diffusion models for structure-based drug design.Proceedings of the AAAI Conference on Artificial Intelligence, 38(11):12671–12679, Mar.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Binding-adaptive diffusion models for structure-based drug design.Proceedings of the AAAI Conference on Artificial Intelligence, 38(11):12671–12679, Mar

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.630069Z

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Observation 6381dd37-bce7-4a21-8686-a099313f71c0 · outbound

This paper cites An effective fragment-based dual conditional diffusion framework for molecular generation.Briefings in Bioinformatics, 27(1): bbaf727, 01 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints An effective fragment-based dual conditional diffusion framework for molecular generation.Briefings in Bioinformatics, 27(1): bbaf727, 01 2026

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.496751Z

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Observation 9c254156-ac2e-45b9-9f93-af8c37fd1479 · outbound

This paper cites Berman, John Westbrook, Zukang Feng, Gary Gilliland, T.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Berman, John Westbrook, Zukang Feng, Gary Gilliland, T

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Observation ac2e1cbd-3be5-46c4-8c57-57bdbe7c6621 · outbound

This paper cites Nourse, W.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Nourse, W

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.360664Z

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Observation eb8a7901-3e2a-4501-a303-223812503b59 · outbound

This paper cites nach0: multimodal natural and chemical languages foundation model.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints nach0: multimodal natural and chemical languages foundation model

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:10.344483Z

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Observation d353b1e0-27e2-4481-9d47-e7630c3349fc · outbound

This paper cites Meireles, and Ivet Bahar.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Meireles, and Ivet Bahar

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.225831Z

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Observation 7d1e3636-ae7a-434f-ac9b-18e05534b8fc · outbound

This paper cites Scalfani, Daniel Probst, Kazuya Ujihara, guillaume godin, Rachel Walker, Juuso Lehtivarjo, Axel Pahl, Francois Berenger, jasondbiggs, and strets123.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Scalfani, Daniel Probst, Kazuya Ujihara, guillaume godin, Rachel Walker, Juuso Lehtivarjo, Axel Pahl, Francois Berenger, jasondbiggs, and strets123

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Observation 612d2de1-0207-4bbb-b728-476e95b932da · outbound

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unresolved cited work

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:10.784992Z

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Observation 3f0f8103-4647-47b7-beea-68bf6e46cf8d · outbound

This paper cites ProLIF: a library to encode molecular interactions as fingerprints.Journal of Cheminformatics, 13(1):72, Sep 2021.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints ProLIF: a library to encode molecular interactions as fingerprints.Journal of Cheminformatics, 13(1):72, Sep 2021

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Resolution: verified exact; doi, observed 2026-08-01T15:58:31.106689Z

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Observation ae5eb126-ba4d-4837-b104-9b0e5aa39d47 · outbound

This paper cites On the art of compiling and using ’drug-like’ chemical fragment spaces.ChemMedChem, 3(10):1503–1507,.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints On the art of compiling and using ’drug-like’ chemical fragment spaces.ChemMedChem, 3(10):1503–1507,

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Observation 3c1b9f49-3940-460f-baab-e1f344e27c00 · outbound

This paper cites Ligand- based pharmacophore modeling using novel 3d pharmacophore signatures.Molecules, 23 (12), 2018.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Ligand- based pharmacophore modeling using novel 3d pharmacophore signatures.Molecules, 23 (12), 2018

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correction dated 2019-03-18. Source: crossref record 10.3390/molecules24061052->10.3390/molecules23123094:correction, observed 2026-07-11T03:04:44.841104+00:00. This notice travels one citation hop only.

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This paper cites GPT-5.5 system card, April 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints GPT-5.5 system card, April 2026

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints GPT-5.4 thinking system card, March 2026

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This paper cites System card: Claude opus 4.7, April 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints System card: Claude opus 4.7, April 2026

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:11.761908Z

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints System card: Claude opus 4.6, February 2026

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:11.908215Z

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Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints System card: Claude sonnet 4.6, February 2026

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:11.986685Z

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Observation 1373986f-98b1-4af5-8b5e-f207eb3442d4 · outbound

This paper cites Gemini 3.1 pro model card, February 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Gemini 3.1 pro model card, February 2026

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Observation 7bd45712-9659-493b-89ed-049aa5ca54a1 · outbound

This paper cites Grok 4.1 model card, November 2025.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Grok 4.1 model card, November 2025

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.114287Z

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Observation cf22a1f1-7c81-4279-82ff-6aad48dcadaa · outbound

This paper cites Qwen3.5: Towards native multimodal agents, February 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Qwen3.5: Towards native multimodal agents, February 2026

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.249837Z

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Observation 6aabf71d-150f-42ac-af54-4001d5d157b8 · outbound

This paper cites DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.377796Z

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Observation b407df51-82a4-446d-aa52-942e7cd169f0 · outbound

This paper cites GLM-5: from Vibe Coding to Agentic Engineering.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints GLM-5: from Vibe Coding to Agentic Engineering

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.562331Z

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Observation d30c2560-1032-403a-91d4-27ef0c81fb03 · outbound

This paper cites Unified modeling of 3d molecular generation via atomic interactions with pocketXMol.Cell, 189(7):1904–1922.e28, Apr 2026.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Unified modeling of 3d molecular generation via atomic interactions with pocketXMol.Cell, 189(7):1904–1922.e28, Apr 2026

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Observation 16746110-3cc0-42de-b480-95fe111860b0 · outbound

This paper cites Morris, and Charlotte M.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Morris, and Charlotte M

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.799161Z

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Observation f46b86d1-a1f6-4d76-babf-9d2e80992e8b · outbound

This paper cites Uni- Dock: GPU-accelerated docking enables ultralarge virtual screening.Journal of Chemical Theory and Computation, 19(11):3336–3345, 2023.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Uni- Dock: GPU-accelerated docking enables ultralarge virtual screening.Journal of Chemical Theory and Computation, 19(11):3336–3345, 2023

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:12.959884Z

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Observation 55eb7d5e-385d-4cde-8668-42fe8dab0b48 · outbound

This paper cites URL https://doi.org/10.1021/jm048957q.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints URL https://doi.org/10.1021/jm048957q

Reference 2005

Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:08.433473Z

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Observation 48e26824-502e-42c8-8fc0-90194cb7c76c · outbound

This paper cites URL https://chemistry-europe.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints URL https://chemistry-europe

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Resolution: unresolved; no resolver link, observed 2026-08-01T15:54:11.195695Z

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This paper cites Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files.

Do Language Models Dream of Binding Molecules? Benchmarking LLMs under Spatial Constraints Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB files

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