Paper Citation Record · LEDGER

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering

As of 17 August 2026, this Paper Citation Record lists 100 of 121 outbound references and 3 inbound Pith citation observations for arXiv:2501.02680.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2501.02680 v1

Coverage vector

measured 100 of 121 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-10T22:12:21.655239Z

measured 103 of 103 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-17T06:30:58.91139+00:00

measured 3 of 3 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-07T04:17:39.671746Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: pith, observed 2026-08-06T23:42:10.084308Z

Reference resolution

100 of 121 outbound references displayed

verified exact2
verified fuzzy41
unresolved56
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 935af85c-be0a-4556-bbe9-c6cc1a656f99 · outbound

This paper cites write newline.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering write newline

Reference 1

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Observation 44c38db8-f1d7-4a3f-8706-30ee7fdf7109 · outbound

This paper cites and Kim, P.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and Kim, P

Reference 2

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Observation 26e03076-114c-4439-b5af-6a0da825cb06 · outbound

This paper cites and Kim, P.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and Kim, P

Reference 3

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Observation 649a3567-70f0-4eca-9c98-1b7c7292cf98 · outbound

This paper cites J., Bambrick, J., Bodenstein, S.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering J., Bambrick, J., Bodenstein, S

Reference 4

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Observation c5fdd4f4-21f6-49d4-9c77-6ceea6cadf77 · outbound

This paper cites X., Fusi, N., Amini, A.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering X., Fusi, N., Amini, A

Reference 5

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Observation a78df140-4cd1-4c2e-ac8e-2c2f73b26388 · outbound

This paper cites X., Fusi, N., Amini, A.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering X., Fusi, N., Amini, A

Reference 6

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Observation 466e262b-30eb-44ac-bcba-7dcf17c2b35f · outbound

This paper cites and G \'o mez-Bombarelli , R.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and G \'o mez-Bombarelli , R

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-10T22:12:16.944842Z

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Observation 3f1b5035-e6e9-4dc3-b9d6-e0989824c7ba · outbound

This paper cites R., Wang, J., Cong, Q., Kinch, L.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering R., Wang, J., Cong, Q., Kinch, L

Reference 8

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Observation e6d56153-ff84-47ae-a240-82ba92198ee2 · outbound

This paper cites E(n) equivariant topological neural networks, July 2024.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering E(n) equivariant topological neural networks, July 2024

Reference 9

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Observation b593097e-76ea-486d-8db7-85d207fe384d · outbound

This paper cites P., Kornbluth, M., Molinari, N., Smidt, T.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering P., Kornbluth, M., Molinari, N., Smidt, T

Reference 10

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Observation 83c7c6de-f0ee-4aa4-bf2e-728dab80422e · outbound

This paper cites Symmetry Group Equivariant Architectures for Physics.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Symmetry Group Equivariant Architectures for Physics

Reference 11

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This paper cites Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges

Reference 12

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Observation ebf188ce-66db-442e-b862-2fc35f9b056c · outbound

This paper cites M., and Deane, C.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering M., and Deane, C

Reference 13

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 14

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Observation 56c55058-211e-4975-ba7e-e24dad5f0084 · outbound

This paper cites An overview of diffusion models: Applications, guided generation, statistical rates and optimization, April 2024 a.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering An overview of diffusion models: Applications, guided generation, statistical rates and optimization, April 2024 a

Reference 15

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Observation e3ddc7fe-4c65-434f-9ac6-9a7630e65d4b · outbound

This paper cites Amp-diffusion: Integrating latent diffusion with protein language models for antimicrobial peptide generation.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Amp-diffusion: Integrating latent diffusion with protein language models for antimicrobial peptide generation

Reference 16

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Observation 413fade7-5d96-4be5-a6f3-2de642dbd67b · outbound

This paper cites Amp-diffusion: Integrating latent diffusion with protein language models for antimicrobial peptide generation, March 2024 c.

Reference 17

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Observation 017b87aa-bcb6-4f32-8c5e-f46a3067c749 · outbound

This paper cites Ilvr: Conditioning method for denoising diffusion probabilistic models.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Ilvr: Conditioning method for denoising diffusion probabilistic models

Reference 18

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Observation 93b2b1fa-72f4-4cfa-a363-24394ec5e6c3 · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 19

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Observation a0b66d6a-199f-4f8e-b4ec-7709df6d0e1c · outbound

This paper cites The discovery of binding modes requires rethinking docking generalization.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering The discovery of binding modes requires rethinking docking generalization

Reference 20

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Observation af221b69-6115-4470-a916-4571c6800b87 · outbound

This paper cites Diffdock: Diffusion steps, twists, and turns for molecular docking, February 2023 b.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Diffdock: Diffusion steps, twists, and turns for molecular docking, February 2023 b

Reference 21

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Observation bdbb1105-edf1-47d0-a019-edf0017ec27e · outbound

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Deep confident steps to new pockets: Strategies for docking generalization

Reference 22

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Observation ab70f958-72e6-4051-91ae-f3be1aae314b · outbound

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering T., and Shah, M

Reference 23

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and Koes, D

Reference 24

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Observation ee97e170-9b02-4d59-b191-27b0cd024f60 · outbound

This paper cites Prottrans: Towards cracking the language of life's code through self-supervised learning, July 2020.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Prottrans: Towards cracking the language of life's code through self-supervised learning, July 2020

Reference 25

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Fabind+: Enhancing molecular docking through improved pocket prediction and pose generation, April 2024 a

Reference 26

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 27

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This paper cites Editorial: Machine learning for peptide structure, function, and design.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Editorial: Machine learning for peptide structure, function, and design

Reference 28

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering D., Uribe-Paredes , R., Olivera-Nappa , \'A ., Navarrete, M

Reference 29

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering W., Peng, X., Su, Y., Peng, J., and Ma, J

Reference 30

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Diffdock-site: A novel paradigm for enhanced protein-ligand predictions through binding site identification

Reference 31

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Observation ebafdfda-9efe-4b5e-b96e-71480119a006 · outbound

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Diffusion models in bioinformatics and computational biology

Reference 32

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This paper cites Continuous automated model evaluation (cameo) complementing the critical assessment of structure prediction in casp12.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Continuous automated model evaluation (cameo) complementing the critical assessment of structure prediction in casp12

Reference 33

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering G., Vignac, C., and Welling, M

Reference 34

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Conditional diffusion based on discrete graph structures for molecular graph generation, May 2023 a

Reference 35

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Learning joint 2d & 3d diffusion models for complete molecule generation, June 2023 b

Reference 36

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Mdm: Molecular diffusion model for 3d molecule generation, September 2022

Reference 37

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering A dual diffusion model enables 3d molecule generation and lead optimization based on target pockets

Reference 38

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering G., Frossard, P., Welling, M., Bronstein, M., and Correia, B

Reference 39

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering B., Baranov, M., Costello, Z., Barber, K

Reference 40

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 41

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models

Reference 43

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering P., Salimans, T., Poole, B., and Ho, J

Reference 44

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 45

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering E., Platen, E., Kloeden, P

Reference 46

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Full-atom peptide design with geometric latent diffusion, May 2024

Reference 47

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This paper cites Pinder: The protein interaction dataset and evaluation resource, July 2024.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Pinder: The protein interaction dataset and evaluation resource, July 2024

Reference 48

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering R., Morey-Burrows, F

Reference 49

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Equivariant graph attention networks for molecular property prediction, March 2022

Reference 50

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Observation 69c0caf7-3129-4af9-946c-0e6a0af8078f · outbound

This paper cites Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation

Reference 51

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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Navigating the design space of equivariant diffusion-based generative models for de novo 3d molecule generation

Reference 52

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Observation c3df153c-d2ac-4635-a60f-71d3618f2a42 · outbound

This paper cites On the generalization properties of diffusion models, January 2024 a.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering On the generalization properties of diffusion models, January 2024 a

Reference 53

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Observation fc6d1331-9deb-4327-bb48-c742d989a6d7 · outbound

This paper cites On the generalization properties of diffusion models, January 2024 b.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering On the generalization properties of diffusion models, January 2024 b

Reference 54

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Observation cde247cc-4fad-4972-b35d-50d1296a7743 · outbound

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Reference 55

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Observation 5d6f9e2d-665c-4810-81d4-aee9db0061c0 · outbound

This paper cites and AlQuraishi, M.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and AlQuraishi, M

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:33.720826Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 6d28d742-6d98-4300-9c1a-7e57fd6a7077 · outbound

This paper cites Out of many, one: Designing and scaffolding proteins at the scale of the structural universe with genie 2, May 2024 b.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Out of many, one: Designing and scaffolding proteins at the scale of the structural universe with genie 2, May 2024 b

Reference 57

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:33.554758Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation d733b116-4316-4f72-98f4-1880b0a68a88 · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 58

Resolution: unresolved; no resolver link, observed 2026-08-10T22:12:19.354851Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 49b22505-4399-4dc9-945a-0c4ae46dc9a2 · outbound

This paper cites L., Gershon, J.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering L., Gershon, J

Reference 59

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:33.284875Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 742b4928-6cee-4a40-86d5-178321251a10 · outbound

This paper cites L., Shijo, S., Bera, A.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering L., Shijo, S., Bera, A

Reference 60

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:33.114756Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation a1a9fcc2-3ffd-4aec-a360-183ad2fddd14 · outbound

This paper cites G., and Zheng, S.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering G., and Zheng, S

Reference 61

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.944917Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 5d2fbdf7-e1d0-4915-8f19-0bb3291c7d23 · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 62

Resolution: unresolved; raw_fallback, observed 2026-08-10T22:12:32.804906Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 095b954a-f85b-4daa-ab48-c8006ce72d0d · outbound

This paper cites Y., Chen, H., and Shen, C.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Y., Chen, H., and Shen, C

Reference 63

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.624761Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 28d9a7e0-7a2a-410e-95f1-dd51d5d39a77 · outbound

This paper cites J., Bau, D., Vullo, A., Walsh, I., and Pollastri, G.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering J., Bau, D., Vullo, A., Walsh, I., and Pollastri, G

Reference 64

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.464750Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 385f9e62-ec45-45bc-ba5a-51649aa99b4c · outbound

This paper cites W., Pitt, W.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering W., Pitt, W

Reference 65

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.335827Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation c1070fa0-306c-4f21-a1a0-83a546d52011 · outbound

This paper cites and Cheng, J.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and Cheng, J

Reference 66

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.242069Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation f7a10070-832d-44d7-b3ee-b850acdfe54c · outbound

This paper cites A brief survey on bio inspired optimization algorithms for molecular docking, July 2014.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering A brief survey on bio inspired optimization algorithms for molecular docking, July 2014

Reference 67

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.150963Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation ddf9849f-effc-4f06-aa8b-5defb5eed538 · outbound

This paper cites S., Mills, J.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering S., Mills, J

Reference 68

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:32.024142Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation be3569d2-d758-48d9-8cf1-46ab58c83875 · outbound

This paper cites L., and Buehler, M.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering L., and Buehler, M

Reference 69

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.824673Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 4ffa3bc5-3aeb-4c25-a417-f20e0b8ee6f5 · outbound

This paper cites L., and Buehler, M.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering L., and Buehler, M

Reference 70

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.654908Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 93431602-e370-4cd6-80c4-d4769ba6792b · outbound

This paper cites Permutation invariant graph generation via score-based generative modeling, March 2020.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Permutation invariant graph generation via score-based generative modeling, March 2020

Reference 71

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.484836Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation ff74557a-9c92-4aff-9212-45c5de1934ff · outbound

This paper cites Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules

Reference 72

Resolution: verified exact; local_arxiv, observed 2026-08-10T22:12:23.514755Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 5dd2aafd-ab09-441d-b2ae-80cdce07d7d5 · outbound

This paper cites and Xie, S.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering and Xie, S

Reference 73

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.351352Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 0903dd48-7f13-4646-8d40-9437b7793d76 · outbound

This paper cites Fabind: Fast and accurate protein-ligand binding, January 2024.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Fabind: Fast and accurate protein-ligand binding, January 2024

Reference 74

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.211054Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation e44b6e78-cad8-4ac9-ba9a-deeabaae3f4b · outbound

This paper cites Moldiff: Addressing the atom-bond inconsistency problem in 3d molecule diffusion generation, May 2023.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Moldiff: Addressing the atom-bond inconsistency problem in 3d molecule diffusion generation, May 2023

Reference 75

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:31.104139Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation e164df2c-a5c0-4822-b3df-fa9998d23faa · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 76

Resolution: unresolved; raw_fallback, observed 2026-08-10T22:12:31.004916Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 93164486-763a-4960-98b6-2588f6cf321f · outbound

This paper cites O., Jamasb, A., Mahmood, O., Sresht, V., and Saremi, S.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering O., Jamasb, A., Mahmood, O., Sresht, V., and Saremi, S

Reference 77

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:30.864846Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 698fd8a8-93f7-4569-b3ff-54d92c704aa5 · outbound

This paper cites F., and Anandkumar, A.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering F., and Anandkumar, A

Reference 78

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:30.714759Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation dac1e891-9373-4769-9f07-5a888f53774b · outbound

This paper cites O., Rupp, M., and Von Lilienfeld, O.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering O., Rupp, M., and Von Lilienfeld, O

Reference 79

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:30.567083Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 39f49f39-2b11-4b44-9753-b47cdba72811 · outbound

This paper cites High-resolution image synthesis with latent diffusion models, April 2022.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering High-resolution image synthesis with latent diffusion models, April 2022

Reference 80

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:30.449237Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 70d3d462-b493-44a5-9b48-97d511466a51 · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 81

Resolution: unresolved; raw_fallback, observed 2026-08-10T22:12:30.323740Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation daeae042-4a34-4298-871b-76bbc8474223 · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 82

Resolution: unresolved; raw_fallback, observed 2026-08-10T22:12:30.175219Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation d2296fdb-11d8-42bc-a24f-4dc44a66da5f · outbound

This paper cites G., Hoogeboom, E., and Welling, M.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering G., Hoogeboom, E., and Welling, M

Reference 83

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:30.024836Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 5898e329-aba3-4fd4-a79c-fb0062ec69a5 · outbound

This paper cites Structure-based drug design with equivariant diffusion models, June 2023.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Structure-based drug design with equivariant diffusion models, June 2023

Reference 84

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:29.844935Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 0f28283c-f4c8-4bfe-b8ec-4fcdae4c981c · outbound

This paper cites VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification

Reference 85

Resolution: unresolved; no resolver link, observed 2026-08-10T22:12:20.928575Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation c7990c3d-7deb-4eba-98c9-278de9cefc55 · outbound

This paper cites Denoising diffusion implicit models, October 2022.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Denoising diffusion implicit models, October 2022

Reference 86

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:29.684755Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 2fb555c2-9630-48c9-9cbd-4f3f929e334c · outbound

This paper cites Score-Based Generative Modeling through Stochastic Differential Equations.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Score-Based Generative Modeling through Stochastic Differential Equations

Reference 87

Resolution: unresolved; no resolver link, observed 2026-08-10T22:12:21.011295Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 8d48f5c4-4e8d-490f-b9ce-f9631618d039 · outbound

This paper cites A survey of generative ai for de novo drug design: new frontiers in molecule and protein generation.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering A survey of generative ai for de novo drug design: new frontiers in molecule and protein generation

Reference 88

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:29.494920Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation a5f9a697-048c-449d-9c11-b686601fe9ad · outbound

This paper cites A survey of generative ai for de novo drug design: New frontiers in molecule and protein generation.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering A survey of generative ai for de novo drug design: New frontiers in molecule and protein generation

Reference 89

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:29.304757Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation d496f79f-5028-4111-9a87-b9698e624bdd · outbound

This paper cites L., Yim, J., Tischer, D., Baker, D., Broderick, T., Barzilay, R., and Jaakkola, T.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering L., Yim, J., Tischer, D., Baker, D., Broderick, T., Barzilay, R., and Jaakkola, T

Reference 90

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:29.144779Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation e241a19b-376b-4640-8b20-37594813ef45 · outbound

This paper cites P., Yumoto, A., Ito, Y., Uzawa, T., and Tsuda, K.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering P., Yumoto, A., Ito, Y., Uzawa, T., and Tsuda, K

Reference 91

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.993583Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 9cfad1bc-c96d-4c48-94f0-1962edec5d95 · outbound

This paper cites an unresolved cited work.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Unresolved cited work

Reference 92

Resolution: unresolved; raw_fallback, observed 2026-08-10T22:12:28.805204Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 2be44aff-b05d-4466-921c-5e542e46f53c · outbound

This paper cites Digress: Discrete denoising diffusion for graph generation, May 2023 a.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Digress: Discrete denoising diffusion for graph generation, May 2023 a

Reference 93

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.624838Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 8a97bbe0-ebf7-4b9a-b9d3-7c18befc2a4d · outbound

This paper cites Midi: Mixed graph and 3d denoising diffusion for molecule generation, June 2023 b.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Midi: Mixed graph and 3d denoising diffusion for molecule generation, June 2023 b

Reference 94

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.472266Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation e4bb4b9b-14d6-41aa-be95-c38801bfe62b · outbound

This paper cites Deep generative models for peptide design.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Deep generative models for peptide design

Reference 95

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.314173Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 5d008fbf-e4d2-4437-94e6-5627ef05ebe9 · outbound

This paper cites Pdb-struct: A comprehensive benchmark for structure-based protein design.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Pdb-struct: A comprehensive benchmark for structure-based protein design

Reference 96

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.174759Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 01d857d2-8764-4d16-8968-3fe8c886f8f6 · outbound

This paper cites Therapeutic peptides: Current applications and future directions.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Therapeutic peptides: Current applications and future directions

Reference 97

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:28.014886Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 06a357ef-1892-4259-b0e5-61158a6d2bec · outbound

This paper cites Diff-amp: Tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Diff-amp: Tailored designed antimicrobial peptide framework with all-in-one generation, identification, prediction and optimization

Reference 98

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:27.864835Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Observation 6747c029-47af-46ae-96c3-0dc56d87e0e3 · outbound

This paper cites DPLM-2: A Multimodal Diffusion Protein Language Model.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering DPLM-2: A Multimodal Diffusion Protein Language Model

Reference 99

Resolution: unresolved; no resolver link, observed 2026-08-10T22:12:21.604147Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 45c4d10f-3597-4f0b-9ced-e8e6ff1bd0ba · outbound

This paper cites Diffusion language models are versatile protein learners, February 2024 c.

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering Diffusion language models are versatile protein learners, February 2024 c

Reference 100

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T22:12:27.734886Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.

Pith citing papers

Observation 8843187c-3200-414f-ab24-8494e0b42bac · inbound

The Effect of Stochasticity in Score-Based Diffusion Sampling: a KL Divergence Analysis cites this paper.

The Effect of Stochasticity in Score-Based Diffusion Sampling: a KL Divergence Analysis From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-07T04:17:39.671746Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 22e1333c-b972-4049-b05b-bb4a58cd6efb · inbound

Geometric deep learning assists protein engineering. Opportunities and Challenges cites this paper.

Geometric deep learning assists protein engineering. Opportunities and Challenges From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering

Reference 83

Resolution: unresolved; no resolver link, observed 2026-08-06T23:48:26.239174Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5a5e2f9b-d114-4581-8707-3a6ffbaee389 · inbound

EHCube4P: Learning Epistatic Patterns Through Hypercube Graph Convolution Neural Network for Protein Fitness Function Estimation cites this paper.

EHCube4P: Learning Epistatic Patterns Through Hypercube Graph Convolution Neural Network for Protein Fitness Function Estimation From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering

Reference 5

Resolution: metadata mismatch; local_arxiv, observed 2026-08-06T23:42:10.214752Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-17T06:30:58.91139+00:00.