Paper Citation Record · LEDGER

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

As of 19 August 2026, this Paper Citation Record lists 43 of 43 outbound references and 0 inbound Pith citation observations for arXiv:2605.27413.

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

pith.paper-citation-record.v1
2605.27413 v1

Coverage vector

measured 43 of 43 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-06-30T19:47:43.387879Z

measured 43 of 43 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-19T06:32:44.657259+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

43 of 43 outbound references displayed

verified exact1
verified fuzzy35
unresolved6
parse uncertain0
malformed identifier1
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 991e61cb-09cb-4f4c-aa77-7b20e2dcfa46 · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 1

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.122914Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation e06ae744-e0f3-480d-ab63-3707c3057814 · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 2

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.125985Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation e655db5d-bf89-40e6-b127-ca8f7677066d · outbound

This paper cites Watson, David Juergens, Nathaniel R.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Watson, David Juergens, Nathaniel R

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.120388Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 85180b69-6a4d-49ef-be60-e72fc1d41f5c · outbound

This paper cites Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus S.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus S

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.092551Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation b78e1b24-b749-427c-8925-84e8a01de7ae · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 5

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.117686Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation e7dba2f9-8cb3-43a6-b098-79ec1c56f303 · outbound

This paper cites Full-atom protein pocket design via iterative refinement.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Full-atom protein pocket design via iterative refinement

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.089620Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 01ebe2a5-17cc-4209-a43a-c946b8b5a7a5 · outbound

This paper cites Efficient generation of protein pockets with PocketGen.Nature Machine Intelligence, 6(11):1382–1395, November 2024.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Efficient generation of protein pockets with PocketGen.Nature Machine Intelligence, 6(11):1382–1395, November 2024

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.095930Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 475e43fd-eb15-4f1d-a342-a5f896c49694 · outbound

This paper cites La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching, July 2025.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching, July 2025

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.114931Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation a2bc9db0-71a9-4707-ab5e-1d1231f45c07 · outbound

This paper cites Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, and Karsten Kreis.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, and Karsten Kreis

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.102003Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation b91b8da0-433d-4ef8-aac4-5e2ac42d2094 · outbound

This paper cites Moses, Alex X.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Moses, Alex X

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.079566Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation a544e248-bed0-461e-8f4a-8e4dbd78b188 · outbound

This paper cites Diffusion language models are versatile protein learners.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Diffusion language models are versatile protein learners

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.132286Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation f2108405-c210-49ae-b051-ac485520df6d · outbound

This paper cites DPLM- 2: A multimodal diffusion protein language model.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design DPLM- 2: A multimodal diffusion protein language model

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.073856Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 13abb8d3-c503-42df-acd0-c93d1f1bc1ed · outbound

This paper cites Elucidating the design space of multimodal protein language models.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Elucidating the design space of multimodal protein language models

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.076779Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 9db7e85b-cd0a-4414-a38c-fad446bdd47b · outbound

This paper cites Remasking discrete diffusion models with inference-time scaling.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Remasking discrete diffusion models with inference-time scaling

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.086697Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation f85febcd-62b0-4d20-a60c-6efacd799aa1 · outbound

This paper cites Block diffusion: Interpolating between autoregressive and diffusion language models.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Block diffusion: Interpolating between autoregressive and diffusion language models

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.070931Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 6a554de8-7560-4001-bfd8-f938734db40e · outbound

This paper cites Large language diffusion models.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Large language diffusion models

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.064566Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation a8ed3fdd-c431-4e71-8e6d-2e1bcae06d81 · outbound

This paper cites Kakade, and Sitan Chen.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Kakade, and Sitan Chen

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.067711Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 8c1627dd-bcc2-4485-a037-1faac119f05f · outbound

This paper cites Dauparas, I.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Dauparas, I

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.083465Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation a53af2bd-4a33-46d7-8f32-6b9ac9a209c6 · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 19

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.098843Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation d2a2adb7-8158-47d1-a18d-03a4e7a4eccb · outbound

This paper cites Hauptmann, Boqing Gong, Ming-Hsuan Yang, Irfan Essa, David A.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Hauptmann, Boqing Gong, Ming-Hsuan Yang, Irfan Essa, David A

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.105786Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 3a904c3e-b6a0-41fb-a34c-c16984720fcf · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 21

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.128879Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation cc28ccfb-fb2a-4e63-890f-46c15a078700 · outbound

This paper cites GCP-VQV AE: A geometry-complete language for protein 3d structure.bioRxiv, 2025.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design GCP-VQV AE: A geometry-complete language for protein 3d structure.bioRxiv, 2025

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.061495Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 422fb88b-cb09-44fc-a1a7-f9d2c9512be2 · outbound

This paper cites Uni-mol: A universal 3d molecular representation learning framework.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Uni-mol: A universal 3d molecular representation learning framework

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.043204Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation cbd474fd-62ff-4913-89fd-eb51107da04d · outbound

This paper cites Learned conformational space and pharmacophore into molecular foundational model.Advanced Science, 13(17):e13556, 2026.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Learned conformational space and pharmacophore into molecular foundational model.Advanced Science, 13(17):e13556, 2026

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.040216Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation de9322d9-b1dc-42d2-b8e4-b675a3185b7f · outbound

This paper cites Molca: Molecular graph-language modeling with cross-modal projector and uni-modal adapter.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Molca: Molecular graph-language modeling with cross-modal projector and uni-modal adapter

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.050248Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 8c358649-2a81-4c78-bb29-4b1e49a9c1c0 · outbound

This paper cites NEXT-MOL: 3d diffusion meets 1d language modeling for 3d molecule generation.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design NEXT-MOL: 3d diffusion meets 1d language modeling for 3d molecule generation

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.028790Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 2fda738e-8c91-4536-9ac4-1231a885b588 · outbound

This paper cites Towards unified and lossless latent space for 3d molecular latent diffusion modeling.arXiv preprint arXiv:2503.15567, 2025.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Towards unified and lossless latent space for 3d molecular latent diffusion modeling.arXiv preprint arXiv:2503.15567, 2025

Reference 27

Resolution: verified exact; arxiv_id, observed 2026-06-30T19:55:01.682834Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 5bb1da44-2a71-487c-b0f4-92c578f881e8 · outbound

This paper cites Prott3: Protein-to-text generation for text-based protein understanding.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Prott3: Protein-to-text generation for text-based protein understanding

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.032999Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation eacf33d6-84c6-4328-bffc-2fdde55e8ea7 · outbound

This paper cites A reparameterized discrete diffusion model for text generation.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design A reparameterized discrete diffusion model for text generation

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.022574Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation c466fd2a-3525-47a9-9702-5e7b59357c64 · outbound

This paper cites Sahoo, Marianne Arriola, Yair Schiff, Aaron Gokaslan, Edgar Marroquin, Justin T.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Sahoo, Marianne Arriola, Yair Schiff, Aaron Gokaslan, Edgar Marroquin, Justin T

Reference 30

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.018615Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation bbd1c2ff-330a-49ae-9625-00a269d851f6 · outbound

This paper cites an unresolved cited work.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Unresolved cited work

Reference 31

Resolution: unresolved; raw_fallback, observed 2026-07-07T23:04:15.025500Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation e4379ba7-7190-4896-a138-069951844cfd · outbound

This paper cites Protenix-v1: Toward high-accuracy open-source biomolecular structure prediction.bioRxiv, 2026.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Protenix-v1: Toward high-accuracy open-source biomolecular structure prediction.bioRxiv, 2026

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.036569Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 74c1f5eb-ab14-4057-87a2-d2e0894d0db4 · outbound

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

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design PLINDER: The protein-ligand interactions dataset and resource

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.010799Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 847e5155-2fdf-48de-af41-f44c281eadf0 · outbound

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

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B

Reference 34

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.057400Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation bd246fa7-5aeb-45fa-8f3a-169197017ca5 · outbound

This paper cites Carlson, and Teresa Head-Gordon.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Carlson, and Teresa Head-Gordon

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:14.992725Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation cb640f72-0bd5-4d12-8d96-99c016dc1f0a · outbound

This paper cites Hekkelman, Ida de Vries, Robbie P.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Hekkelman, Ida de Vries, Robbie P

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.003167Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 8a33252b-7fde-42f0-b7ca-fbdc221c45df · outbound

This paper cites Ballard, Joshua Bambrick, Sebastian W.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Ballard, Joshua Bambrick, Sebastian W

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.014757Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 89d22d81-2604-43bd-9aa4-83e986899ebf · outbound

This paper cites Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature Biotechnology, 35(11):1026–1028, November 2017.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature Biotechnology, 35(11):1026–1028, November 2017

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.007395Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 53562896-b81e-45cc-a7b3-5ee2bd155b27 · outbound

This paper cites Gomez, Lukasz Kaiser, and Illia Polosukhin.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Gomez, Lukasz Kaiser, and Illia Polosukhin

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.047023Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation ba64c322-e68f-4028-8e1a-48a9d297fd7b · outbound

This paper cites Evolutionary-scale prediction of atomic- level protein structure with a language model.Science, 379(6637):1123–1130.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Evolutionary-scale prediction of atomic- level protein structure with a language model.Science, 379(6637):1123–1130

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:14.996782Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 41027119-1d9d-47be-8e91-867726b9d9e4 · outbound

This paper cites Scoring function for automated assessment of protein structure template quality.Proteins: Structure, Function, and Bioinformatics, 57(4):702–710.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Scoring function for automated assessment of protein structure template quality.Proteins: Structure, Function, and Bioinformatics, 57(4):702–710

Reference 41

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.000070Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation dfb6ab8a-4a1c-4206-82aa-14ada1f91001 · outbound

This paper cites Maiorov and Gordon M.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Maiorov and Gordon M

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-07-07T23:04:15.053083Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Observation 7d52c06b-c23e-445e-934f-2ae63562d1fe · outbound

This paper cites Tillack, and Stefano Forli.

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design Tillack, and Stefano Forli

Reference 43

Resolution: malformed identifier; raw_fallback, observed 2026-07-07T23:04:15.110994Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-19T06:32:44.657259+00:00.

Pith citing papers

No inbound Pith citation observations are available.