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DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.20.576370Source: DataRank Database

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model is a research paper published in bioRxiv (Cold Spring Harbor Laboratory) (2024). On theSindex it has a DataRank of 0.543. It has been cited 9 times, with 8 citing works in its 1-hop citation network.

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0.543DataRank · unranked

Scored on demand from live citation data

Open Access9 citations · 8 citing works in its network

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›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (7 grants)OA: greenTopics (21)Linked Datasets (3)DataCite Reuse (3)IDs (PubMed, OpenAlex)

FAIR Checklist

Context only (not used in score)

Findable (2/2)

Has DOI
Indexed in repositories

Accessible (1/2)

Open Access

Interoperable (2/2)

DataCite relations
Linked datasets

Reusable (0/3)

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DataRank Breakdown

Base Score 64%Citation Network 36%

Base Score Contribution

0.345

From this paper's citation signal

Citation Network Contribution

0.198

From 6 citing papers with measurable signal

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Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 8 citers.

CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps
bioRxiv (Cold Spring Harbor Laboratory)20242 citations13 referencesContributes 0.085
AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network
bioRxiv (Cold Spring Harbor Laboratory)202513 citations69 referencesContributes 0.038
Improved model building for cryo-EM maps using local attention and 3D rotary position embedding
bioRxiv (Cold Spring Harbor Laboratory)20249 citations62 referencesContributes 0.037
Structural insights into MERS and SARS coronavirus membrane proteins
Communications Biology20252 citations34 referencesContributes 0.032
Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data
Structure202426 citations147 referencesContributes 0.022

Authors (5)

Zhu Han ORCID,Genki Terashi ORCID,Manav Taluja ORCID,Daisuke Kihara ORCID,Xiao Wang ORCID

Live enrichment

PubMed:38328203 OpenAlex:https://openalex.org/W4391151488

National Science Foundation

Grant: 2003635

IIBR Informatics: Development of Multimodal approaches for protein function prediction

National Science Foundation

Grant: 1825941

Nanomanufacturing of Protein Macromolecular Frameworks Through an Integrated Bioengineering and Computational Approach

National Science Foundation

Grant: 1925643

Collaborative Research: RoL: Revealing a new mechanism of action for eukaryotic transcriptional activation domains

National Science Foundation

Grant: 2146026

Collaborative Research: Identification and Structural Modeling of Intrinsically Disordered Protein-Protein and Protein-Nucleic Acids Interactions

National Institutes of Health

Grant: 1R01GM133840-01A1

Building protein structure models for intermediate resolution cryo-electron microscopy maps

National Science Foundation

Grant: 2151678

Collaborative Research: Integrated Moment-Based Descriptors and Deep Neural Network for Screening Three-Dimensional Biological Data

NIGMS NIH HHS

Grant: R01 GM133840

greenLicense: cc-by-nc-nd

repositoryhttps://www.biorxiv.org/content/biorxiv/early/2024/02/28/2024.01.20.576370.full.pdf

GREENhttps://www.biorxiv.org/content/biorxiv/early/2024/02/28/2024.01.20.576370.full.pdf

repositoryhttps://www.biorxiv.org/content/biorxiv/early/2024/02/28/2024.01.20.576370.full.pdf

publisherhttps://syndication.highwire.org/content/doi/10.1101/2024.01.20.576370

repositoryhttps://doi.org/10.1101/2024.01.20.576370

Fields of Study

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionProtein Structure and DynamicsMedicineBiologyComputer ScienceMaterials Science0206 medical engineering02 engineering and technology

Keywords

DiffusionResolution (logic)Low resolutionStatistical physicsHigh resolutionPhysicsGeologyComputer scienceThermodynamicsRemote sensingArtificial intelligenceArticle

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

10.5281/zenodo.12155184Zenodo

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

10.5281/zenodo.10714882Zenodo

DiffModeler: Large Macromolecular Structure Modeling in Low-Resolution Cryo-EM Maps Using Diffusion Model

10.5281/zenodo.10714883Zenodo