Search Results - "Burley SK"

Multi-scale structural similarity embedding search across entire proteomes.

Authors: Segura J Sanchez-Garcia R Bittrich S et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Feb 28; Vol. 42 (3).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.

Authors: Wood-Charlson EM Åkerström WN Anderson L et al.

Source: Communications biology [Commun Biol] 2026 Jul 18; Vol. 9 (1). Date of Electronic Publication: 2026 Jul 18.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Publishing Group UK Country of Publication: England NLM ID: 101719179 Publication Model: Electronic Cited Medium: Internet ISSN: 2399-3642 (Electronic) Linking ISSN: 23993642 NLM ISO Abbreviation: Commun Biol Subsets: MEDLINE

IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.

Authors: Zalevsky AO Vallat B Webb BM et al.

Source: Journal of molecular biology [J Mol Biol] 2026 Sep 15; Vol. 438 (18), pp. 169598. Date of Electronic Publication: 2025 Dec 18.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.

Authors: Tauriello G Lill Y Sgrignani J et al.

Source: Journal of molecular biology [J Mol Biol] 2026 Sep 15; Vol. 438 (18), pp. 169658. Date of Electronic Publication: 2026 Jan 22.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: Netherlands NLM ID: 2985088R Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1089-8638 (Electronic) Linking ISSN: 00222836 NLM ISO Abbreviation: J Mol Biol Subsets: MEDLINE

Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution.

Authors: Feng Z Balasubramaniyan B Bekker GJ et al.

Source: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2026 Aug 01. Date of Electronic Publication: 2026 Aug 01.

Publication Type: Journal Article

Journal Info: Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101676043 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2059-7983 (Electronic) Linking ISSN: 20597983 NLM ISO Abbreviation: Acta Crystallogr D Struct Biol Subsets: MEDLINE

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.

Authors: Midlik A Bittrich S Fleming JR et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jul 07; Vol. 53 (W1), pp. W408-W414.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Where and how to house big data on small fragments.

Authors: Erlanson DA Burley SK Fearon D et al.

Source: Nature communications [Nat Commun] 2025 May 05; Vol. 16 (1), pp. 4179. Date of Electronic Publication: 2025 May 05.

Publication Type: Journal Article; Review

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

The NMR Exchange Format (NEF): Specification and Applications.

Authors: Płoskoń E Baskaran K Tejero R et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Apr 24. Date of Electronic Publication: 2026 Apr 24.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

MolViewStories: Interactive molecular storytelling.

Authors: Slanináková T Charlop-Powers Z Doshchenko V et al.

Source: Protein science : a publication of the Protein Society [Protein Sci] 2026 Apr; Vol. 35 (4), pp. e70540.

Publication Type: Journal Article

Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.

Authors: Bittrich S Rose AS Sehnal D et al.

Source: Protein science : a publication of the Protein Society [Protein Sci] 2025 Apr; Vol. 34 (4), pp. e70093.

Publication Type: Journal Article

Journal Info: Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE

Protein Data Bank (PDB): Fifty-three years young and having a transformative impact on science and society.

Authors: Berman HM Burley SK

Source: Quarterly reviews of biophysics [Q Rev Biophys] 2025 Feb 20; Vol. 58, pp. e9. Date of Electronic Publication: 2025 Feb 20.

Publication Type: Journal Article; Review; Historical Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, N.I.H., Extramural

Journal Info: Publisher: Cambridge Univ. Press Country of Publication: England NLM ID: 0144032 Publication Model: Electronic Cited Medium: Internet ISSN: 1469-8994 (Electronic) Linking ISSN: 00335835 NLM ISO Abbreviation: Q Rev Biophys Subsets: MEDLINE

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank.

Authors: Burley SK Bhatt R Bhikadiya C et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D564-D574.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Authors: Liu T Hwang L Burley SK et al.

Source: Nucleic acids research [Nucleic Acids Res] 2025 Jan 06; Vol. 53 (D1), pp. D1633-D1644.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

PDX1 phosphorylation at S61 by mTORC1 links nutrient signaling to β cell function and metabolic disease.

Authors: Fan J Zhang X Zhang J et al.

Source: Cell reports [Cell Rep] 2026 Jan 27; Vol. 45 (1), pp. 116811. Date of Electronic Publication: 2026 Jan 12.

Publication Type: Journal Article

Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101573691 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2211-1247 (Electronic) NLM ISO Abbreviation: Cell Rep Subsets: MEDLINE

OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.

Authors: Tariq MU Sheshadri N Shen J et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2026 Jan 26. Date of Electronic Publication: 2026 Jan 26.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.

Authors: Vallat B Rose Y Piehl DW et al.

Source: Nucleic acids research [Nucleic Acids Res] 2026 Jan 06; Vol. 54 (D1), pp. D489-D498.

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit.

Authors: Bittrich S Midlik A Varadi M et al.

Source: Current protocols [Curr Protoc] 2024 Jul; Vol. 4 (7), pp. e1099.

Publication Type: Journal Article

Journal Info: Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101773894 Publication Model: Print Cited Medium: Internet ISSN: 2691-1299 (Electronic) Linking ISSN: 26911299 NLM ISO Abbreviation: Curr Protoc Subsets: MEDLINE

RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.

Authors: Bittrich S Segura J Duarte JM et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2024 Jun 03; Vol. 40 (6).

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.

Authors: Choudhary P Feng Z Berrisford J et al.

Source: Database : the journal of biological databases and curation [Database (Oxford)] 2024 May 27; Vol. 2024.

Publication Type: Journal Article; Research Support, Non-U.S. Gov't

Journal Info: Publisher: Oxford Journals Country of Publication: England NLM ID: 101517697 Publication Model: Print Cited Medium: Internet ISSN: 1758-0463 (Electronic) Linking ISSN: 17580463 NLM ISO Abbreviation: Database (Oxford) Subsets: MEDLINE

Matrix Metalloproteinases as Candidate Antigenic Determinants for Anti-Tumor Autoantibodies in Human Ovarian Cancer: A Post Hoc Analysis.

Authors: Markosian C Ille AM Burley SK et al.

Source: FASEB journal : official publication of the Federation of American Societies for Experimental Biology [FASEB J] 2025 Sep 30; Vol. 39 (18), pp. e71066.

Publication Type: Journal Article

Journal Info: Publisher: Federation of American Societies for Experimental Biology Country of Publication: United States NLM ID: 8804484 Publication Model: Print Cited Medium: Internet ISSN: 1530-6860 (Electronic) Linking ISSN: 08926638 NLM ISO Abbreviation: FASEB J Subsets: MEDLINE