Paper Citation Record · LEDGER

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

As of 9 August 2026, this Paper Citation Record lists 100 of 100 outbound references and 9 inbound Pith citation observations for arXiv:2502.09565.

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

pith.paper-citation-record.v1
2502.09565 v1

Coverage vector

measured 100 of 100 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T21:06:31.081687Z

measured 109 of 109 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-09T06:31:02.800959+00:00

measured 9 of 9 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-07T11:07:08.771596Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-07-04T02:49:24.158985Z

Reference resolution

100 of 100 outbound references displayed

verified exact17
verified fuzzy35
unresolved41
parse uncertain0
malformed identifier6
metadata mismatch1

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 9103ed96-5361-444f-a78b-d04645f84d2d · outbound

This paper cites Applications of molecular dynamics simulation in protein study.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Applications of molecular dynamics simulation in protein study

Reference 1

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Source-reported events for the cited work

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Observation dba6151b-2a33-47a6-b182-273b91d2f47c · outbound

This paper cites Molecular dynamics simulations of biomolecules.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Molecular dynamics simulations of biomolecules

Reference 2

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.725599Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation aecc71f3-b5e8-4b96-86b2-1cb5c9021275 · outbound

This paper cites Molecular dynamics simulation for all.Neuron, 99(6):1129–1143, 2018.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Molecular dynamics simulation for all.Neuron, 99(6):1129–1143, 2018

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.729564Z

Source-reported events for the cited work

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Observation 40df9882-9512-4ebb-81c0-54dad82815dc · outbound

This paper cites The protein data bank archive.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models The protein data bank archive

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.733736Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 8abc7d18-cea5-4828-a6a0-3d354761a9da · outbound

This paper cites CHARMM: the biomolecular simulation program.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models CHARMM: the biomolecular simulation program

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.738057Z

Source-reported events for the cited work

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Observation 043c7e06-3075-48a7-acf4-aafc66658b15 · outbound

This paper cites Force fields for protein simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Force fields for protein simulations

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.741316Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 873b5748-b774-4867-ae2b-abee828175f5 · outbound

This paper cites Baumgartner and Hongzhou Zhang.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Baumgartner and Hongzhou Zhang

Reference 7

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.744883Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5c32eb60-72ed-49b0-823a-aa171722f7e9 · outbound

This paper cites RadonPy: automated physical prop- erty calculation using all-atom classical molecular dynamics simulations for polymer informatics.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models RadonPy: automated physical prop- erty calculation using all-atom classical molecular dynamics simulations for polymer informatics

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.748020Z

Source-reported events for the cited work

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Observation 3e522570-8d6f-437a-aa6c-8716496a4c52 · outbound

This paper cites Gmx qk: An automated protein protein- ligand complex simulation workflow bridged to MM PBSA, based on gromacs and zenity-dependent GUI for beginners in MD simulation study.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Gmx qk: An automated protein protein- ligand complex simulation workflow bridged to MM PBSA, based on gromacs and zenity-dependent GUI for beginners in MD simulation study

Reference 9

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.751306Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e15f5474-2243-4201-a821-e640358ed440 · outbound

This paper cites Simulation foundry: Automated and F.A.I.R.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Simulation foundry: Automated and F.A.I.R

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.754431Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a435e132-a358-4ad9-be93-59d064fd1f5a · outbound

This paper cites CHAPERONg: A tool for automated GROMACS-based molecular dynamics simu- lations and trajectory analyses.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models CHAPERONg: A tool for automated GROMACS-based molecular dynamics simu- lations and trajectory analyses

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.757484Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 89500277-5236-4c99-bb21-185ccbfe0861 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.760908Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b1db7c02-8040-46e3-b2de-d3fbb82c47bc · outbound

This paper cites Giese, and Darrin M.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Giese, and Darrin M

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.764108Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e1441baa-5232-4f72-8d8f-d919a0b7bd85 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.767337Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e4028e15-9ff6-461b-b5c4-082c56aaec5c · outbound

This paper cites Bhati, James Suter, James Hetherington, Stefan J.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Bhati, James Suter, James Hetherington, Stefan J

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.770514Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2d7b64b9-1342-43f4-8d43-8e9c649ae484 · outbound

This paper cites Cino, and Rafaela Salgado Ferreira.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Cino, and Rafaela Salgado Ferreira

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.774255Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 80b0fe22-a244-4804-997a-28f0519829c8 · outbound

This paper cites Bodnarchuk, Russell Viner, Ian D.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Bodnarchuk, Russell Viner, Ian D

Reference 17

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.777753Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1196b1c8-e19a-4284-9267-fe8ce1ca97f3 · outbound

This paper cites EasyAmber: A comprehensive toolbox to auto- mate the molecular dynamics simulation of proteins.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models EasyAmber: A comprehensive toolbox to auto- mate the molecular dynamics simulation of proteins

Reference 18

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.781356Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a803ba8f-9d3c-4fa6-9f5d-d08754c60b9c · outbound

This paper cites PACKMOL: A package for building initial configurations for molecular dynamics simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models PACKMOL: A package for building initial configurations for molecular dynamics simulations

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.785230Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation ad8adf37-232f-4c9c-9881-032c40b8595e · outbound

This paper cites MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models MDAnalysis: a toolkit for the analysis of molecular dynamics simulations

Reference 20

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.788917Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1cb1ff0e-72a2-4d3f-a60a-66b78878c766 · outbound

This paper cites McGibbon, Kyle A.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models McGibbon, Kyle A

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.190513Z

Source-reported events for the cited work

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Observation 747167d8-9c15-49ef-89d9-b730355cdb29 · outbound

This paper cites OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.178173Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 0c4f975b-c95e-40d8-ac2a-5750354fcfdd · outbound

This paper cites GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.165807Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 8fcc36b4-1f38-4386-878c-72fca9be3173 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 24

Resolution: unresolved; raw_fallback, observed 2026-08-07T21:06:32.152384Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 30c098e9-9b75-4323-aac5-6f87ee1d068b · outbound

This paper cites MDANSE: An interactive analysis environment for molecular dynamics simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models MDANSE: An interactive analysis environment for molecular dynamics simulations

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.139426Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation b69cd9a1-9db4-48e7-bb3f-fa542f07bba3 · outbound

This paper cites QwikMD - gateway for easy simulation with VMD and NAMD.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models QwikMD - gateway for easy simulation with VMD and NAMD

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.127187Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 4ebcc143-64c7-4797-b7f3-1cbbb772eac2 · outbound

This paper cites MDWiZ: a platform for the automated translation of molecular dynamics simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models MDWiZ: a platform for the automated translation of molecular dynamics simulations

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.113742Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 83eff7e3-e044-4d95-b6ee-0b8de62edd5b · outbound

This paper cites Bringing molecular dynamics simulation data into view.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Bringing molecular dynamics simulation data into view

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.099642Z

Source-reported events for the cited work

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Observation f191e9b1-a039-461a-8d6e-dc8b6312992a · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 29

Resolution: unresolved; raw_fallback, observed 2026-08-07T21:06:32.087173Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation e7d47e2b-4424-4c73-b94d-17d1181f50f9 · outbound

This paper cites VMD: visual molecular dynamics.Journal of molecular graphics, 14(1):33–38, 1996.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models VMD: visual molecular dynamics.Journal of molecular graphics, 14(1):33–38, 1996

Reference 30

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.073768Z

Source-reported events for the cited work

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Observation 5af9d450-5035-4dd4-a739-7682b536c87d · outbound

This paper cites Gromita: a fully integrated graphical user interface to gromacs 4.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Gromita: a fully integrated graphical user interface to gromacs 4

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.060456Z

Source-reported events for the cited work

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Observation b7976428-2d67-4fc6-abab-4d6ce67df5d9 · outbound

This paper cites PlayMolecule ProteinPrepare: a web applica- tion for protein preparation for molecular dynamics simulations.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models PlayMolecule ProteinPrepare: a web applica- tion for protein preparation for molecular dynamics simulations

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.047349Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 995a9f48-9d49-4cb4-ade0-e09f3b8c7f46 · outbound

This paper cites Toolformer: Language Models Can Teach Themselves to Use Tools.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Toolformer: Language Models Can Teach Themselves to Use Tools

Reference 33

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Observation e1a9c86b-584b-4e37-911c-986230e856b3 · outbound

This paper cites MRKL Systems: A modular, neuro-symbolic architecture that combines large language models, external knowledge sources and discrete reasoning.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models MRKL Systems: A modular, neuro-symbolic architecture that combines large language models, external knowledge sources and discrete reasoning

Reference 34

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Source-reported events for the cited work

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Observation 72777fa6-80f1-4d24-bc30-b52247ebd4a3 · outbound

This paper cites ReAct: Synergizing Reasoning and Acting in Language Models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models ReAct: Synergizing Reasoning and Acting in Language Models

Reference 35

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Source-reported events for the cited work

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Observation 6e7920a1-695e-4797-93dc-24ae6b7955ae · outbound

This paper cites Aviary: training language agents on challenging scientific tasks.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Aviary: training language agents on challenging scientific tasks

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.848762Z

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Observation 8965ddf0-58f5-4195-b044-ebd010f95a46 · outbound

This paper cites BioGPT: generative pre-trained transformer for biomedical text generation and mining.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models BioGPT: generative pre-trained transformer for biomedical text generation and mining

Reference 37

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.033685Z

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Observation 0e6da3dc-d362-4a2c-9c2d-b67912a6aed8 · outbound

This paper cites Large language models encode clinical knowledge.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Large language models encode clinical knowledge

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.019942Z

Source-reported events for the cited work

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Observation 311a6b7c-302c-41f8-85dd-4778e846037d · outbound

This paper cites Empowering biomedical discovery with AI agents.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Empowering biomedical discovery with AI agents

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:32.004871Z

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Observation 70917651-ec05-4c96-bb1e-425853727322 · outbound

This paper cites Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D White, and Philippe Schwaller.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D White, and Philippe Schwaller

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.989817Z

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Observation 5673000c-6af6-4090-a356-d7e0c8a61754 · outbound

This paper cites Autonomous chemical research with large language models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Autonomous chemical research with large language models

Reference 41

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Observation b23fcc7f-8952-43b7-918f-f1956774d4c0 · outbound

This paper cites CACTUS: A computational framework for generating realistic white matter microstructure substrates, 2023.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models CACTUS: A computational framework for generating realistic white matter microstructure substrates, 2023

Reference 42

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.969195Z

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Observation fdcc61b8-80d0-48e9-b4bd-5599a7d006d5 · outbound

This paper cites 14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models 14 examples of how LLMs can transform materials science and chemistry: a reflection on a large language model hackathon

Reference 43

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.957442Z

Source-reported events for the cited work

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Observation 7290b398-9270-4030-87f4-d3ea4fe6e751 · outbound

This paper cites Automation and machine learning augmented by large language models in catalysis study.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Automation and machine learning augmented by large language models in catalysis study

Reference 44

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.945359Z

Source-reported events for the cited work

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Observation 23acfc3e-87c5-4d32-9e2f-3cc662d92a77 · outbound

This paper cites LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillation.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillation

Reference 45

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Source-reported events for the cited work

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Observation b306630d-6aa7-4d5a-b83b-ede942aa7e9a · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Large language models for inorganic synthesis predictions

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.932661Z

Source-reported events for the cited work

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Observation 6699990d-d717-43ad-9ef9-2f0f023be449 · outbound

This paper cites Harnessing Large Language Model to collect and analyze Metal-organic framework property dataset.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Harnessing Large Language Model to collect and analyze Metal-organic framework property dataset

Reference 47

Resolution: verified exact; local_arxiv, observed 2026-08-07T21:06:31.555005Z

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Observation e4924885-a3c8-4771-bc05-dd066ae34584 · outbound

This paper cites Language agents achieve superhuman synthesis of scientific knowledge.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Language agents achieve superhuman synthesis of scientific knowledge

Reference 48

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.888497Z

Source-reported events for the cited work

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Observation 92d3de2e-8401-4b97-a815-10b9c27fb403 · outbound

This paper cites Prince, Henry Chan, Aikaterini Vriza, Tao Zhou, Varuni K.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Prince, Henry Chan, Aikaterini Vriza, Tao Zhou, Varuni K

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.919491Z

Source-reported events for the cited work

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Observation 766d8f93-6780-4dce-a2f3-f4d02c835179 · outbound

This paper cites Bioplanner: Automatic evaluation of llms on protocol planning in biology, 2023.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Bioplanner: Automatic evaluation of llms on protocol planning in biology, 2023

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.907230Z

Source-reported events for the cited work

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Observation d27c8e87-c849-4b29-8e63-ddc48cde57f7 · outbound

This paper cites Johnson, Di Yin, Mihir Shah, Denny Zhou, Russ Altman, Mengdi Wang, and Le Cong.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Johnson, Di Yin, Mihir Shah, Denny Zhou, Russ Altman, Mengdi Wang, and Le Cong

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.893476Z

Source-reported events for the cited work

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Observation b9a8f084-51b9-4796-b424-2a74322e35ab · outbound

This paper cites Accelerated end-to-end chemical synthesis development with large language models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Accelerated end-to-end chemical synthesis development with large language models

Reference 52

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.880662Z

Source-reported events for the cited work

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Observation 04c76e98-91a2-4e72-8072-fbaaa8abc91b · outbound

This paper cites ChatMOF: an artificial intelligence system for predicting and generating metal- organic frameworks using large language models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models ChatMOF: an artificial intelligence system for predicting and generating metal- organic frameworks using large language models

Reference 53

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.868110Z

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Observation b66db214-16bf-4629-8207-f17b4f54d1f9 · outbound

This paper cites Anywhere: A multi-agent framework for reliable and diverse foreground-conditioned image inpainting, 2024.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Anywhere: A multi-agent framework for reliable and diverse foreground-conditioned image inpainting, 2024

Reference 54

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.854531Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 0d6e20ec-166f-422d-97b4-671366a16539 · outbound

This paper cites Ghafarollahi and M.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Ghafarollahi and M

Reference 55

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.842129Z

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Observation 15cf5672-2a59-4575-bf54-ee9a13ea84f9 · outbound

This paper cites A review of large language models and autonomous agents in chemistry.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models A review of large language models and autonomous agents in chemistry

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.830403Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation b527674d-2d73-4643-afcf-66f4ec44fc1c · outbound

This paper cites LangChain, 10 2022.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models LangChain, 10 2022

Reference 57

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.920961Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation dd7d164b-3edf-489c-a081-9785616be3c6 · outbound

This paper cites UniProt: the Universal Protein Knowledgebase in 2023.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models UniProt: the Universal Protein Knowledgebase in 2023

Reference 58

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.812849Z

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Observation c55da60a-1481-42f7-8b52-c700cd277159 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models molrender

Reference 59

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.801130Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 80a56ca2-f7d9-4ba4-ad6f-890ae1c2fdd2 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models NGLview–interactive molecular graphics for Jupyter note- books

Reference 60

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.789863Z

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Observation b3b639bc-2e33-4ebf-b7e1-952c29cec197 · outbound

This paper cites Training language models to follow instructions with human feedback.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Training language models to follow instructions with human feedback

Reference 61

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.935486Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d8bd9d57-9d4f-4187-8c64-48097c6a07b5 · outbound

This paper cites GPT-4 Technical Report.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models GPT-4 Technical Report

Reference 62

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.939227Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a167dd19-eeb0-4a34-b1b7-b435ec645200 · outbound

This paper cites The Llama 3 Herd of Models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models The Llama 3 Herd of Models

Reference 63

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.942885Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e5f44d43-e092-4c91-a622-354901ca6449 · outbound

This paper cites [Accessed 24-01-2025].

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models [Accessed 24-01-2025]

Reference 64

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.772235Z

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Observation b9cf5463-553a-4735-9e9e-28c2531743f2 · outbound

This paper cites https://www-cdn.anthropic.com/fed9cc193a14b84131812372d8d5857f8f304c52/ Model_Card_Claude_3_Addendum.pdf.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models https://www-cdn.anthropic.com/fed9cc193a14b84131812372d8d5857f8f304c52/ Model_Card_Claude_3_Addendum.pdf

Reference 65

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.762572Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation f7e6a060-6ebe-4ad7-9a35-757866916086 · outbound

This paper cites The Claude 3 model family: Opus, Sonnet, Haiku, Mar 2024.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models The Claude 3 model family: Opus, Sonnet, Haiku, Mar 2024

Reference 66

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.751829Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 971066b9-ff41-438f-a4d2-8b9df23a7787 · outbound

This paper cites OpenAI o1 System Card.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models OpenAI o1 System Card

Reference 67

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.957274Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b62aefcc-17a7-4ca3-b5fe-2bb5dc7445b6 · outbound

This paper cites GPT-4o System Card.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models GPT-4o System Card

Reference 68

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.961774Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation f6f17934-5da6-42ac-99ed-86d2cf0a36d0 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models LAB-Bench: Measuring Capabilities of Language Models for Biology Research

Reference 69

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.965744Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 74e1d195-cd68-4291-a051-12d462403b28 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models MLLM-Tool: A multimodal large language model for tool agent learning, 2024

Reference 70

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.740994Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 09e1a8e1-1331-499c-9cbe-c3e53a70365f · outbound

This paper cites AssistGPT: A general multi-modal assistant that can plan, execute, inspect, and learn, 2023.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models AssistGPT: A general multi-modal assistant that can plan, execute, inspect, and learn, 2023

Reference 71

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.729662Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 3a769a25-c74e-43bc-90a6-b69a607c1755 · outbound

This paper cites Voyager: An Open-Ended Embodied Agent with Large Language Models.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Voyager: An Open-Ended Embodied Agent with Large Language Models

Reference 72

Resolution: unresolved; no resolver link, observed 2026-08-07T21:06:30.977254Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 8e5b596f-3d76-4e4a-81dc-da1370f7c1ed · outbound

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Reference 73

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Observation 23b2c6b5-6af1-4587-91e3-e5741bc45dba · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 74

Resolution: malformed identifier; raw_fallback, observed 2026-08-07T21:06:31.707682Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 9e16f625-5d2e-40f2-9598-2be21a1fb7ea · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 75

Resolution: malformed identifier; raw_fallback, observed 2026-08-07T21:06:31.695873Z

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Observation 54a89be1-5dcb-45e5-9dee-30ed5aafe8c6 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 76

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.292708Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation b13f9a19-b764-4042-90ed-a49bf5e164c0 · outbound

This paper cites 3389/fbinf.2023.1125479.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models 3389/fbinf.2023.1125479

Reference 77

Resolution: metadata mismatch; raw_fallback, observed 2026-08-07T21:06:31.458372Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation c24485dc-53f6-4924-a1e8-23cbeb515968 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 78

Resolution: malformed identifier; raw_fallback, observed 2026-08-07T21:06:31.683831Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation fb8cecdc-f47f-4846-9638-ef2a57d0775d · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 79

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.280401Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 686a57ab-c763-4e81-aad6-2a3abf3512ab · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 80

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.268977Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation a87db576-4ef9-474b-9c5b-07be776e6c88 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 81

Resolution: verified exact; raw_fallback, observed 2026-08-07T21:06:31.378331Z

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Observation a8498d36-98e6-4f7d-9e13-eeb24acfc8d4 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 82

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.257437Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation f3632931-c6d8-4d00-90aa-ad8e2887b9d7 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 83

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.246746Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 83f9548b-8a09-4be0-844c-bfa20f716fc4 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 84

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.235409Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 34362ee7-e5f1-4a23-aeb1-6aeaa35aa1c0 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 85

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Unavailable: canonical work link unavailable.

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 86

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.216982Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation fb1f41a3-2345-4c10-91d7-f939e243afce · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 87

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.205240Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 10f11931-bb1a-4fd5-bf06-defb274e8933 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 88

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Observation 4ea8c4f1-26e8-4f50-bc6a-292815ecce6b · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 89

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.193463Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 8d02f19a-ce64-4769-80b4-5ea1bbb3a270 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 90

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.182708Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation bafabea1-247f-4932-88c5-2962d0e9d3ce · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 91

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.172045Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 4ddf52fd-2ca3-4c33-a2cd-b6d7d2595fc2 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 92

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.161590Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 09bb1cb4-b05a-4f98-b4f9-819e05aeb25b · outbound

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Reference 93

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Observation a15d44a3-d9be-4c19-bf32-ecbeec8b3a26 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models 1038/s41598-017-18328-4

Reference 94

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T21:06:31.646942Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation d8fd7926-56d5-43a5-8312-86cba0ebabdf · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 95

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.150153Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 554bd89d-00dd-4689-93e5-8dba3d9a49bd · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 96

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.136282Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 558fb3b6-dc31-4665-a344-c5ea6c44eda9 · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 97

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Unavailable: canonical work link unavailable.

Observation 51400267-afdc-4787-94d4-318a3dc01239 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 98

Resolution: verified exact; doi, observed 2026-08-07T21:06:31.115670Z

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 18b33c8f-3a7e-4179-aed5-8502c6e04bb1 · outbound

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MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 99

Resolution: unresolved; raw_fallback, observed 2026-08-07T21:06:31.635361Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 477efe58-8b57-4dc6-9a0a-2f3c6acfa3bb · outbound

This paper cites an unresolved cited work.

MDCrow: Automating Molecular Dynamics Workflows with Large Language Models Unresolved cited work

Reference 100

Resolution: unresolved; raw_fallback, observed 2026-08-07T21:06:31.622900Z

Source-reported events for the cited work

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Pith citing papers

Observation 8d1f7792-88db-4553-af29-5e1121d2260e · inbound

ChemGraph: An Agentic Framework for Computational Chemistry Workflows cites this paper.

ChemGraph: An Agentic Framework for Computational Chemistry Workflows MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 9

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Unavailable: canonical work link unavailable.

Observation 7138bfa3-ce80-47f3-a56d-88c08992472c · inbound

Automating MD simulations for Proteins using Large language Models: NAMD-Agent cites this paper.

Automating MD simulations for Proteins using Large language Models: NAMD-Agent MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 20

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a99e1454-58fb-4d61-a9c7-811a11d83f60 · inbound

El Agente Quntur: A research collaborator agent for quantum chemistry cites this paper.

El Agente Quntur: A research collaborator agent for quantum chemistry MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 65

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 005a9a3e-3489-4d87-832f-3ef582cf422b · inbound

From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry cites this paper.

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Reference 240

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No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 85f376cf-da50-424e-a800-75a7debb7264 · inbound

ChatMOSP: A Chemistry-Grounded Mobile Agent for Working-State Catalyst Simulations cites this paper.

ChatMOSP: A Chemistry-Grounded Mobile Agent for Working-State Catalyst Simulations MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 35

Resolution: verified exact; arxiv_id, observed 2026-06-30T14:44:45.653335Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 60938991-7a84-4875-a5ef-ae6456156a5a · inbound

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches cites this paper.

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 23

Resolution: verified exact; arxiv_id, observed 2026-07-01T20:56:14.476959Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation fe0bd20f-3f73-4305-9d2b-0f68d12f7473 · inbound

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches cites this paper.

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 26

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:35:34.130014Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 882963c6-4ee8-43bb-9db4-16cabe4eb1fd · inbound

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback cites this paper.

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 1

Resolution: verified exact; arxiv_id, observed 2026-07-03T14:18:22.726648Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation e12b7579-91aa-4035-9068-567f3592c0f4 · inbound

LLM-Guided Test-Time Discovery of Quantum-Chemical Approximation Algorithms cites this paper.

LLM-Guided Test-Time Discovery of Quantum-Chemical Approximation Algorithms MDCrow: Automating Molecular Dynamics Workflows with Large Language Models

Reference 20

Resolution: verified exact; arxiv_id, observed 2026-07-04T02:49:24.160647Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.