Paper Citation Record · LEDGER

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

As of 10 August 2026, this Paper Citation Record lists 61 of 61 outbound references and 1 inbound Pith citation observation for arXiv:2607.09998.

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

pith.paper-citation-record.v1
2607.09998 v1

Coverage vector

measured 61 of 61 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-07-14T01:09:51.800413Z

measured 62 of 62 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-10T06:31:04.303077+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-01T03:21:02.702990Z

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

61 of 61 outbound references displayed

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External citation measurements

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Outbound references

Observation 53d8b3c6-6b8a-42cb-a4e1-ea64644f612b · outbound

This paper cites Macrocycles in drug discovery - learning from the past for the future.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Macrocycles in drug discovery - learning from the past for the future

Reference 1

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Observation 021544e6-3623-4f95-93f6-89f717d2b079 · outbound

This paper cites Macrocycles for conventionally druggable targets: lessons from macrocyclic kinase inhibitors.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Macrocycles for conventionally druggable targets: lessons from macrocyclic kinase inhibitors

Reference 2

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Observation a045e18f-4896-4b03-8a6b-5fc0f53e4cc5 · outbound

This paper cites Accurate de novo design of hyperstable constrained peptides.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate de novo design of hyperstable constrained peptides

Reference 3

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Observation 0d62024c-52d9-4e4c-a4ab-cab7df647df7 · outbound

This paper cites Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate de novo design of high-affinity protein-binding macrocycles using deep learning

Reference 4

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Observation 67705862-3398-4580-aaeb-f30e88871422 · outbound

This paper cites De novo design of protein structure and function with RFdiffusion.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design De novo design of protein structure and function with RFdiffusion

Reference 5

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Observation 3d7309d0-94e0-404c-a0ab-2a729f9c7ab6 · outbound

This paper cites Expansive discovery of chemically diverse structured macrocyclic oligoamides.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Expansive discovery of chemically diverse structured macrocyclic oligoamides

Reference 6

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Observation e9ea2953-be7e-4f47-b83d-d6c166a794aa · outbound

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Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Unresolved cited work

Reference 7

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Observation d5370191-806a-4418-bb3d-1ed372cbf57c · outbound

This paper cites Boltz-2: Towards accurate and efficient binding affinity prediction.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Boltz-2: Towards accurate and efficient binding affinity prediction

Reference 8

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Observation 1b24feb6-6bb6-4042-b050-37d07eafdc0b · outbound

This paper cites Accelerating biomolecular modeling with atomworks and rf3.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accelerating biomolecular modeling with atomworks and rf3

Reference 9

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Observation 14ee9449-df8c-4a25-b651-c9d5400ae9e7 · outbound

This paper cites RareFold: Structure prediction and design of proteins with noncanonical amino acids.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design RareFold: Structure prediction and design of proteins with noncanonical amino acids

Reference 10

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Observation e8eecfb5-60bf-432b-85b1-3fc3c6193204 · outbound

This paper cites Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3

Reference 11

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Observation f54ff1ad-f732-4945-969d-55f1eb49a832 · outbound

This paper cites Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2

Reference 12

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Observation bd85d7a2-10f4-4b82-9678-451e9d7eccb1 · outbound

This paper cites NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design NCPepFold: Accurate Prediction of Noncanonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation

Reference 13

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Observation 91ed6571-fe77-46f7-9937-07d6f25b0e69 · outbound

This paper cites Improving accuracy, diversity, and speed with prime macrocycle conformational sampling.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Improving accuracy, diversity, and speed with prime macrocycle conformational sampling

Reference 14

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Observation 8b563db7-a407-4474-a178-58cb72813e8f · outbound

This paper cites Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen

Reference 15

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Observation c01b8fd7-ff37-4c80-9d11-a2098c3dc414 · outbound

This paper cites Elucidating solution structures of cyclic peptides using molecular dynamics simulations.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Elucidating solution structures of cyclic peptides using molecular dynamics simulations

Reference 16

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Observation 965da832-9716-4743-8bc6-ede4bc035eec · outbound

This paper cites Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate structure prediction of biomolecular interactions with AlphaFold 3

Reference 17

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Observation 789a3191-b3a2-4086-b45e-3b4bc896641a · outbound

This paper cites Modeling protein–small molecule conformational ensembles with PLACER.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Modeling protein–small molecule conformational ensembles with PLACER

Reference 18

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Observation d5510d45-765f-44ad-9a13-38dd4763dffb · outbound

This paper cites Proteina: Scaling Flow-based Protein Structure Generative Models.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Proteina: Scaling Flow-based Protein Structure Generative Models

Reference 19

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Observation 5e26d044-d110-4e3d-b49e-625dcd4e178b · outbound

This paper cites Highly accurate protein structure prediction with AlphaFold.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Highly accurate protein structure prediction with AlphaFold

Reference 20

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Observation 968bd7c3-9f96-428e-9250-af64fb9be6da · outbound

This paper cites Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Reference 21

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Observation 26d94371-22a8-4f4d-b7d2-64d005faf714 · outbound

This paper cites CycPeptMPDB: a comprehensive database of membrane permeability of cyclic peptides.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design CycPeptMPDB: a comprehensive database of membrane permeability of cyclic peptides

Reference 22

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Observation e123de75-fa39-4b3e-b235-920583caa6e9 · outbound

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Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Unresolved cited work

Reference 23

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Observation 67fc7769-59cb-481a-9a8a-17e9d0028dbe · outbound

This paper cites MolMeDB: molecules on membranes database.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design MolMeDB: molecules on membranes database

Reference 24

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Observation 33d59b57-38c1-4ff6-8dc1-8898a9560ec7 · outbound

This paper cites The NCATS Pharmaceutical Collection: a 10-year update.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design The NCATS Pharmaceutical Collection: a 10-year update

Reference 25

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Observation d5f74228-d6d0-4526-bd03-216535b23b82 · outbound

This paper cites PerMM: a web tool and database for analysis of passive membrane permeability and translocation pathways of bioactive molecules.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design PerMM: a web tool and database for analysis of passive membrane permeability and translocation pathways of bioactive molecules

Reference 26

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Observation f9a5cd55-444c-4c18-a8a1-5f281efa6408 · outbound

This paper cites Conformational effects on the passive membrane permeability of synthetic macrocycles.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Conformational effects on the passive membrane permeability of synthetic macrocycles

Reference 27

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Observation c44cb244-52d2-4afe-bfdb-36fcd508bf52 · outbound

This paper cites SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design SIMPD: an algorithm for generating simulated time splits for validating machine learning approaches

Reference 28

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Observation 650463ac-aff1-477e-ae76-c6ee0b2e5aff · outbound

This paper cites The Cambridge structural database.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design The Cambridge structural database

Reference 29

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Observation 655ee870-9cc0-46c6-8139-46a1a7d233e2 · outbound

This paper cites Accurate de novo design of membrane-traversing macrocycles.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate de novo design of membrane-traversing macrocycles

Reference 30

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Observation 70c6b9cf-3cf8-4a9f-bb56-207040cf070c · outbound

This paper cites Cyclic peptide structure prediction and design using AlphaFold2.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Cyclic peptide structure prediction and design using AlphaFold2

Reference 31

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This paper cites Biotite: a unifying open source computational biology framework in Python.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Biotite: a unifying open source computational biology framework in Python

Reference 32

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This paper cites Version Release 2025 09 4.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Version Release 2025 09 4

Reference 33

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Observation ee65edba-8311-4056-a4fb-d543747e59d0 · outbound

This paper cites High-quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design High-quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators

Reference 34

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Observation 223c7105-22f6-45c5-aee5-8a563a9c965d · outbound

This paper cites Accurate physics-based flexible docking of macrocyclic ligands.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate physics-based flexible docking of macrocyclic ligands

Reference 35

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Observation f51ca35f-bd44-4e84-881d-db17914486aa · outbound

This paper cites Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences

Reference 36

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Observation c007ac0c-c315-4635-a76e-7359161edf78 · outbound

This paper cites Scalable Low-Energy Molecular Conformer Generation with Quantum Mechanical Accuracy.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Scalable Low-Energy Molecular Conformer Generation with Quantum Mechanical Accuracy

Reference 37

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This paper cites Torsional diffusion for molecular conformer generation.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Torsional diffusion for molecular conformer generation

Reference 38

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This paper cites Et-flow: Equivariant flow-matching for molecular conformer generation.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Et-flow: Equivariant flow-matching for molecular conformer generation

Reference 39

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This paper cites Accurate and Efficient Structural Ensemble Generation of Macrocyclic Peptides using Internal Coordinate Diffusion.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Accurate and Efficient Structural Ensemble Generation of Macrocyclic Peptides using Internal Coordinate Diffusion

Reference 40

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This paper cites Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction

Reference 41

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This paper cites Descriptor-based Foundation Models for Molecular Property Prediction.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Descriptor-based Foundation Models for Molecular Property Prediction

Reference 42

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This paper cites Chemprop: a machine learning package for chemical property prediction.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Chemprop: a machine learning package for chemical property prediction

Reference 43

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Observation 5ad24a3b-b982-43a3-8ee4-f88280fa451d · outbound

This paper cites May 2025.doi: 10.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design May 2025.doi: 10

Reference 44

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This paper cites Have protein-ligand co-folding methods moved beyond memorisation?.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Have protein-ligand co-folding methods moved beyond memorisation?

Reference 45

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

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design PLINDER: The protein-ligand interactions dataset and evaluation resource

Reference 46

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This paper cites Deep learning for protein-ligand docking: Are we there yet?.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Deep learning for protein-ligand docking: Are we there yet?

Reference 47

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This paper cites PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences

Reference 48

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This paper cites AIMNet2: a neural network potential to meet your neutral, charged, organic, and elemental-organic needs.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design AIMNet2: a neural network potential to meet your neutral, charged, organic, and elemental-organic needs

Reference 49

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This paper cites The open molecules 2025 (omol25) dataset, evaluations, and models.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design The open molecules 2025 (omol25) dataset, evaluations, and models

Reference 50

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This paper cites Comprehensive computational design of ordered peptide macrocycles.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Comprehensive computational design of ordered peptide macrocycles

Reference 51

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Observation adddca0c-e26f-4da8-a6eb-4f0ad19491f7 · outbound

This paper cites State-selective modulation of heterotrimeric G αs signaling with macrocyclic peptides.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design State-selective modulation of heterotrimeric G αs signaling with macrocyclic peptides

Reference 52

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Observation d6633bdf-cd09-43ef-b82d-820c467838c0 · outbound

This paper cites In vitro selection of macrocyclic peptide inhibitors containing cyclic γ2, 4-amino acids targeting the SARS-CoV-2 main protease.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design In vitro selection of macrocyclic peptide inhibitors containing cyclic γ2, 4-amino acids targeting the SARS-CoV-2 main protease

Reference 53

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This paper cites Approaches for peptide and protein cyclisation.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Approaches for peptide and protein cyclisation

Reference 54

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This paper cites mRNA display: from basic principles to macrocycle drug discovery.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design mRNA display: from basic principles to macrocycle drug discovery

Reference 55

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Observation 67c80025-be75-40a9-917a-75edafcbf35b · outbound

This paper cites RNA display methods for the discovery of bioactive macrocycles.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design RNA display methods for the discovery of bioactive macrocycles

Reference 56

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Observation 5aefa49c-5380-46bd-8563-80a3dc56ea59 · outbound

This paper cites Ultra-large chemical libraries for the discovery of high-affinity peptide binders.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Ultra-large chemical libraries for the discovery of high-affinity peptide binders

Reference 57

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Observation 28e00635-c574-44c7-a1e9-74deda77f967 · outbound

This paper cites The RaPID platform for the discovery of pseudo-natural macrocyclic peptides.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design The RaPID platform for the discovery of pseudo-natural macrocyclic peptides

Reference 58

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Observation f1cfe872-9b31-48ba-af29-900a47e31402 · outbound

This paper cites Macrocyclic DNA-encoded chemical libraries: a historical perspective.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Macrocyclic DNA-encoded chemical libraries: a historical perspective

Reference 59

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Observation 7a79c3e4-3bd3-4baa-b378-bc7c48a625da · outbound

This paper cites Validation of a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design Validation of a new methodology to create oral drugs beyond the rule of 5 for intracellular tough targets

Reference 60

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Observation 313c8a8e-c9a4-47a7-9e0c-f45e1d6dffa4 · outbound

This paper cites De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries.

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design De novo mapping of α-helix recognition sites on protein surfaces using unbiased libraries

Reference 61

Resolution: unresolved; no resolver link, observed 2026-07-14T01:09:51.800413Z

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Pith citing papers

Observation adda6421-9857-437a-9dcc-31f220ede372 · inbound

Accurate structural modeling of chemically diverse molecular interfaces with Vilya-2 cites this paper.

Accurate structural modeling of chemically diverse molecular interfaces with Vilya-2 Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

Reference 23

Resolution: unresolved; no resolver link, observed 2026-08-01T03:21:02.702990Z

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