Paper Citation Record · LEDGER

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design

As of 23 August 2026, this Paper Citation Record lists 35 of 35 outbound references and 0 inbound Pith citation observations for arXiv:2505.21241.

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

pith.paper-citation-record.v1
2505.21241 v1

Coverage vector

measured 35 of 35 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T13:44:35.595456Z

measured 35 of 35 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-23T06:30:58.430688+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

35 of 35 outbound references displayed

verified exact0
verified fuzzy12
unresolved23
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 699e4d55-8096-4822-bcea-710f88d489ee · outbound

This paper cites Accurate structure prediction of biomolecular interactions with alphafold 3.Nature, pages 1–3, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Accurate structure prediction of biomolecular interactions with alphafold 3.Nature, pages 1–3, 2024

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:31.740769Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 29f88295-da17-45cb-acd7-7520ec7266ea · outbound

This paper cites The rosetta all-atom energy function for macromolecular modeling and design.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design The rosetta all-atom energy function for macromolecular modeling and design

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:38.604923Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 489a3a16-c7de-4230-954e-1e4c0965c769 · outbound

This paper cites Accurate prediction of protein–nucleic acid complexes using rosettafoldna.Nature methods, 21(1):117–121, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Accurate prediction of protein–nucleic acid complexes using rosettafoldna.Nature methods, 21(1):117–121, 2024

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:38.413256Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 6032f4ed-f8cb-4f66-81b5-4988a23371e9 · outbound

This paper cites Improving de novo protein binder design with deep learning.Nature Communications, 14(1):2625, 2023.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Improving de novo protein binder design with deep learning.Nature Communications, 14(1):2625, 2023

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:32.049862Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation ff2622b7-0f58-4dc9-9f39-a64d6edd4ccd · outbound

This paper cites Pyrosetta: a script-based interface for implementing molecular modeling algorithms using rosetta.Bioinformatics, 26(5):689–691, 2010.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Pyrosetta: a script-based interface for implementing molecular modeling algorithms using rosetta.Bioinformatics, 26(5):689–691, 2010

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:32.142429Z

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Unavailable: canonical work link unavailable.

Observation 684414e2-d453-4645-ae03-68ab6c30c7fe · outbound

This paper cites Pepmlm: target sequence-conditioned generation of therapeutic peptide binders via span masked language modeling.ArXiv, pages arXiv–2310, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Pepmlm: target sequence-conditioned generation of therapeutic peptide binders via span masked language modeling.ArXiv, pages arXiv–2310, 2024

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:38.206573Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 1e06bfd4-f3cf-478d-8064-440a0e9946ba · outbound

This paper cites Massively parallel de novo protein design for targeted therapeutics.Nature, 550(7674):74–79, 2017.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Massively parallel de novo protein design for targeted therapeutics.Nature, 550(7674):74–79, 2017

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:38.056241Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 474c0926-0bc1-4e99-b9eb-9113c75a5c2c · outbound

This paper cites Boltzde- sign1: Inverting all-atom structure prediction model for generalized biomolecular binder design.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Boltzde- sign1: Inverting all-atom structure prediction model for generalized biomolecular binder design

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:37.855867Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation db40c3ca-1d48-45cb-bdec-eeb339072b5b · outbound

This paper cites Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:32.602892Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e2035b29-148b-4dee-a9e4-bbf19dd73e04 · outbound

This paper cites Protein complex prediction with alphafold-multimer.biorxiv, pages 2021–10, 2021.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Protein complex prediction with alphafold-multimer.biorxiv, pages 2021–10, 2021

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:32.679092Z

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Observation 45b2ed91-955f-4406-be6d-cae6e170500e · outbound

This paper cites Se (3)-transformers: 3d roto-translation equivariant attention networks.Advances in neural information processing systems, 33:1970–1981, 2020.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Se (3)-transformers: 3d roto-translation equivariant attention networks.Advances in neural information processing systems, 33:1970–1981, 2020

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:32.796536Z

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Observation ab7e41ac-88a8-4a14-b8ec-3330c8de04ed · outbound

This paper cites Computational protein design—the next generation tool to expand synthetic biology applications.Current opinion in biotechnology, 52: 145–152, 2018.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Computational protein design—the next generation tool to expand synthetic biology applications.Current opinion in biotechnology, 52: 145–152, 2018

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:37.675777Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation b1de0638-cc8c-4324-87fc-37da9e6c0f1f · outbound

This paper cites Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Your Classifier is Secretly an Energy Based Model and You Should Treat it Like One

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.013383Z

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Unavailable: canonical work link unavailable.

Observation e406ea42-09cd-4d2a-9db5-fd773475db01 · outbound

This paper cites Simulating 500 million years of evolution with a language model.Science, page eads0018, 2025.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Simulating 500 million years of evolution with a language model.Science, page eads0018, 2025

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.133097Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation af3b945b-20ff-402d-819f-e0aa9e6e6741 · outbound

This paper cites Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.279067Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 53ec7674-4f83-444d-8c73-f37e64028505 · outbound

This paper cites Dsmbind: Se (3) denoising score matching for unsupervised binding energy prediction and nanobody design.bioRxiv, pages 2023–12, 2023.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Dsmbind: Se (3) denoising score matching for unsupervised binding energy prediction and nanobody design.bioRxiv, pages 2023–12, 2023

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:37.455487Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 44ea9d64-5ec4-42dc-9cee-80dd712c1e15 · outbound

This paper cites Learning from Protein Structure with Geometric Vector Perceptrons.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Learning from Protein Structure with Geometric Vector Perceptrons

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.471667Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3a62c266-7564-4d44-b698-abaed3bc21aa · outbound

This paper cites Highly accurate protein structure prediction with alphafold.nature, 596(7873):583–589, 2021.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Highly accurate protein structure prediction with alphafold.nature, 596(7873):583–589, 2021

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.635136Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5c83ce40-8ef2-46bf-b540-77745490fb87 · outbound

This paper cites Full-Atom Peptide Design based on Multi-modal Flow Matching.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Full-Atom Peptide Design based on Multi-modal Flow Matching

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.715971Z

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Unavailable: canonical work link unavailable.

Observation e15443d2-3581-47e7-9174-c3028989159d · outbound

This paper cites Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:33.850389Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2d0d2c9a-23f0-46a9-8ce6-df438e7e303b · outbound

This paper cites Ppflow: Target-aware peptide design with torsional flow matching.bioRxiv, pages 2024–03, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Ppflow: Target-aware peptide design with torsional flow matching.bioRxiv, pages 2024–03, 2024

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:37.240754Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 11fd2105-2948-4c43-8ad5-cc5507b68608 · outbound

This paper cites Language models of protein sequences at the scale of evolution enable accurate structure prediction.BioRxiv, 2022: 500902, 2022.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Language models of protein sequences at the scale of evolution enable accurate structure prediction.BioRxiv, 2022: 500902, 2022

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:36.986651Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation b0ab2a41-2e0a-48bd-9158-e3522689bcae · outbound

This paper cites Language models enable zero-shot prediction of the effects of mutations on protein function.Advances in neural information processing systems, 34:29287–29303, 2021.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Language models enable zero-shot prediction of the effects of mutations on protein function.Advances in neural information processing systems, 34:29287–29303, 2021

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:34.184164Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d6fe59c2-3b43-45af-8770-62d1c0ab6de9 · outbound

This paper cites an unresolved cited work.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Unresolved cited work

Reference 24

Resolution: unresolved; raw_fallback, observed 2026-08-07T13:44:36.709188Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation e6ac9247-34bb-434b-aadc-ca2797a47fd0 · outbound

This paper cites RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:34.478468Z

Source-reported events for the cited work

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Observation 69d146bb-9d20-4ae5-ae0f-0ca60ed10045 · outbound

This paper cites Bindcraft: one-shot design of functional protein binders.bioRxiv, pages 2024–09, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Bindcraft: one-shot design of functional protein binders.bioRxiv, pages 2024–09, 2024

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:34.594317Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 060f21e0-8cf9-4b21-8e73-910ab1bd385a · outbound

This paper cites Frame Averaging for Invariant and Equivariant Network Design.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Frame Averaging for Invariant and Equivariant Network Design

Reference 27

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:34.691718Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 497d5840-9348-4ad2-99f3-562e2b5c03ab · outbound

This paper cites E (n) equivariant graph neural networks.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design E (n) equivariant graph neural networks

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:34.820930Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation ad06ac70-4994-44bb-9a9f-56db46df42a4 · outbound

This paper cites The foldx web server: an online force field.Nucleic acids research, 33(suppl_2): W382–W388, 2005.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design The foldx web server: an online force field.Nucleic acids research, 33(suppl_2): W382–W388, 2005

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:36.495129Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 50a3c464-673a-4e57-83f9-74a09995669b · outbound

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

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature biotechnology, 35(11):1026–1028, 2017

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:35.080562Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 28b7358d-7e2b-4ef1-a135-6cb035c44ae1 · outbound

This paper cites Attention is all you need.Advances in Neural Information Processing Systems, 2017.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Attention is all you need.Advances in Neural Information Processing Systems, 2017

Reference 31

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:35.179231Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation fe27fc86-061d-4351-96a1-d751f6529237 · outbound

This paper cites De novo design of protein structure and function with rfdiffusion.Nature, 620(7976):1089–1100, 2023.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design De novo design of protein structure and function with rfdiffusion.Nature, 620(7976):1089–1100, 2023

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:35.247823Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 6deb6052-d6c2-4d1d-a879-d43550f2c6a7 · outbound

This paper cites Boltz-1: Democratizing biomolecular interaction modeling.bioRxiv, pages 2024–11, 2024.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Boltz-1: Democratizing biomolecular interaction modeling.bioRxiv, pages 2024–11, 2024

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:36.234915Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation 885deaee-3058-4e27-9fb4-0732853a647b · outbound

This paper cites Design of high-affinity binders to immune modulating receptors for cancer immunotherapy.Nature Communications, 16(1):2001, 2025.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Design of high-affinity binders to immune modulating receptors for cancer immunotherapy.Nature Communications, 16(1):2001, 2025

Reference 34

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T13:44:35.998892Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-23T06:30:58.430688+00:00.

Observation b41183bd-5426-4197-ad4b-fba32cdd1b51 · outbound

This paper cites De novo design of high-affinity protein binders with AlphaProteo.

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design De novo design of high-affinity protein binders with AlphaProteo

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-07T13:44:35.595456Z

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Unavailable: canonical work link unavailable.

Pith citing papers

No inbound Pith citation observations are available.