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Scopus Author ID: 55990584300

Keywords

structural biology, intrinsic disorder, database development, web application design

Countries

United Kingdom

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Employment (5)

European Bioinformatics Institute: Cambridge, Cambridgeshire, GB

2023-05-02 to present | PDBe Coordinator (Protein Data Bank in Europe)
Employment
Source: Self-asserted source
Mihaly Varadi

European Bioinformatics Institute: Cambridge, Cambridgeshire, GB

2019-10-01 to 2023-05-01 | Project Leader (Protein Data Bank in Europe)
Employment
Source: Self-asserted source
Mihaly Varadi

European Bioinformatics Institute: Cambridge, Cambridgeshire, GB

2015-10-01 to 2019-09-30 | Scientific Programmer (Protein Data Bank in Europe)
Employment
Source: Self-asserted source
Mihaly Varadi

Vrije Universiteit Brussel: Brussel, BE

2011-08-29 to 2015-09-31 | Computational Biologist (Structural Biology Research Center)
Employment
Source: Self-asserted source
Mihaly Varadi

Hungarian Academy of Sciences: Budapest, HU

2010-12-01 to 2011-08-28 | Computational biologist (Institute of Enzymology)
Employment
Source: Self-asserted source
Mihaly Varadi

Education and qualifications (2)

Vrije Universiteit Brussel: Brussel, BE

2012-09-01 to 2016-02-04 | PhD Bioscience-engineering (Structural Biology Research Center)
Education
Source: Self-asserted source
Mihaly Varadi

Szent Istvan Egyetem Allatorvos-tudomanyi Kar: Budapest, HU

2005-09-01 to 2011-05-30 | MSc Applied Zoology
Education
Source: Self-asserted source
Mihaly Varadi

Works (50 of 55)

Items per page:
Page 1 of 2

Challenges in bridging the gap between protein structure prediction and functional interpretation

Proteins: Structure, Function, and Bioinformatics
2025-01 | Journal article
DOI: 10.1002/prot.26614
Contributors: Mihaly Varadi; Maxim Tsenkov; Sameer Velankar
Source: check_circle
Crossref

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

Current Protocols
2024-07 | Journal article
DOI: 10.1002/cpz1.1099
Contributors: Sebastian Bittrich; Adam Midlik; Mihaly Varadi; Sameer Velankar; Stephen K. Burley; Jasmine Y. Young; David Sehnal; Brinda Vallat
Source: check_circle
Crossref

Harnessing the 3D‐Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data

Current Protocols
2024-05 | Journal article
DOI: 10.1002/cpz1.1047
Contributors: Paulyna Magaña; Sreenath Nair; Mihaly Varadi; Sameer Velankar
Source: check_circle
Crossref

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

Database
2024-05-27 | Journal article
DOI: 10.1093/database/baae041
Contributors: Preeti Choudhary; Zukang Feng; John Berrisford; Henry Chao; Yasuyo Ikegawa; Ezra Peisach; Dennis W Piehl; James Smith; Ahsan Tanweer; Mihaly Varadi et al.
Source: check_circle
Crossref

Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies

Structural Dynamics
2024-05-01 | Journal article
DOI: 10.1063/4.0000251
Contributors: Joseph I. J. Ellaway; Stephen Anyango; Sreenath Nair; Hossam A. Zaki; Nurul Nadzirin; Harold R. Powell; Aleksandras Gutmanas; Mihaly Varadi; Sameer Velankar
Source: check_circle
Crossref

MolViewSpec

Zenodo
2024-02-19 | Software
DOI: 10.5281/zenodo.10680551
Contributors: Adam Midlik; Sebastian Bittrich; Mihaly Varadi; Sameer Velankar; Stephen K. Burley; Jasmine Young; Brinda Vallat; David Sehnal
Source: check_circle
DataCite

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.

Nucleic acids research
2024-01 | Journal article
DOI: 10.1093/nar/gkad1088
PMID: 38015445
PMC: PMC10767983
Contributors: Thakur M; Buniello A; Brooksbank C; Gurwitz KT; Hall M; Hartley M; Hulcoop DG; Leach AR; Marques D; Martin M et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.

Nucleic acids research
2024-01 | Journal article
DOI: 10.1093/nar/gkad947
PMID: 37904608
PMC: PMC10767937
Contributors: Ghafouri H; Lazar T; Del Conte A; Tenorio Ku LG; PED Consortium ; Tompa P; Tosatto SCE; Monzon AM
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

Nucleic Acids Research
2024-01-05 | Journal article
DOI: 10.1093/nar/gkad1011
Contributors: Mihaly Varadi; Damian Bertoni; Paulyna Magana; Urmila Paramval; Ivanna Pidruchna; Malarvizhi Radhakrishnan; Maxim Tsenkov; Sreenath Nair; Milot Mirdita; Jingi Yeo et al.
Source: check_circle
Crossref

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.

Scientific data
2023-12 | Journal article
DOI: 10.1038/s41597-023-02778-9
PMID: 38040737
PMC: PMC10692154
Contributors: Appasamy SD; Berrisford J; Gaborova R; Nair S; Anyango S; Grudinin S; Deshpande M; Armstrong D; Pidruchna I; Ellaway JIJ et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.

Journal of cheminformatics
2023-12 | Journal article
DOI: 10.1186/s13321-023-00786-w
PMID: 38042830
PMC: PMC10693035
Contributors: Kunnakkattu IR; Choudhary P; Pravda L; Nadzirin N; Smart OS; Yuan Q; Anyango S; Nair S; Varadi M; Velankar S
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBImages: a command-line tool for automated macromolecular structure visualization

Bioinformatics
2023-12-01 | Journal article
DOI: 10.1093/bioinformatics/btad744
Contributors: Adam Midlik; Sreenath Nair; Stephen Anyango; Mandar Deshpande; David Sehnal; Mihaly Varadi; Sameer Velankar; Xin Gao
Source: check_circle
Crossref

PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank

2023-10 | Preprint
DOI: 10.1101/2023.10.24.563739
PPR: PPR748627
Contributors: Choudhary P; Feng Z; Berrisford J; Chao H; Ikegawa Y; Peisach E; Piehl DW; Smith J; Tanweer A; Varadi M et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Clustering-predicted structures at the scale of the known protein universe.

Nature
2023-09 | Journal article
DOI: 10.1038/s41586-023-06510-w
PMID: 37704730
Contributors: Barrio-Hernandez I; Yeo J; Jänes J; Mirdita M; Gilchrist CLM; Wein T; Varadi M; Velankar S; Beltrao P; Steinegger M
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

2023-08 | Preprint
DOI: 10.1101/2023.08.04.552003
PPR: PPR703570
Contributors: Kunnakkattu IR; Choudhary P; Pravda L; Nadzirin N; Smart OS; Yuan Q; Anyango S; Nair S; Varadi M; Velankar S
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Automated Pipeline for Comparing Protein Conformational States in the PDB to AlphaFold2 Predictions

2023-07 | Preprint
DOI: 10.1101/2023.07.13.545008
PPR: PPR690709
Contributors: Ellaway JIJ; Anyango S; Nair S; Zaki HA; Nadzirin N; Powell HR; Gutmanas A; Varadi M; Velankar S
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Challenges in Bridging the Gap Between Protein Structure Prediction and Functional Interpretation

2023-06-30 | Preprint
DOI: 10.22541/au.168810664.47717663/v1
Contributors: Mihaly Varadi; Maxim Tsenkov; Sameer Velankar
Source: check_circle
Crossref

Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data

2023-05 | Preprint
DOI: 10.1101/2023.05.15.540692
PPR: PPR660660
Contributors: Appasamy SD; Berrisford J; Gaborova R; Nair S; Anyango S; Grudinin S; Deshpande M; Armstrong D; Pidruchna I; Ellaway JIJ et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Clustering predicted structures at the scale of the known protein universe

2023-04 | Preprint
DOI: 10.21203/rs.3.rs-2727632/v1
PPR: PPR643683
Contributors: Steinegger M; Beltrao P; Velankar S; Varadi M; Wein T; Gilchrist C; Mirdita M; Jänes J; Yeo J; Barrio-Hernandez I
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

Current Opinion in Structural Biology
2023-04 | Journal article
DOI: 10.1016/j.sbi.2023.102543
Contributors: Mihaly Varadi; Nicola Bordin; Christine Orengo; Sameer Velankar
Source: check_circle
Crossref

Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.

Scientific data
2023-04 | Journal article
DOI: 10.1038/s41597-023-02101-6
PMID: 37045837
PMC: PMC10097656
Contributors: Choudhary P; Anyango S; Berrisford J; Tolchard J; Varadi M; Velankar S
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Clustering predicted structures at the scale of the known protein universe

2023-03 | Preprint
DOI: 10.1101/2023.03.09.531927
PPR: PPR628389
Contributors: Barrio-Hernandez I; Yeo J; Jänes J; Wein T; Varadi M; Velankar S; Beltrao P; Steinegger M
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

Journal of molecular biology
2023-02 | Journal article
DOI: 10.1016/j.jmb.2023.168021
PMID: 36828268
Contributors: Vallat B; Tauriello G; Bienert S; Haas J; Webb BM; Žídek A; Zheng W; Peisach E; Piehl DW; Anischanka I et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models

2022-12 | Preprint
DOI: 10.1101/2022.12.06.518550
PPR: PPR581884
Contributors: Vallat B; Tauriello G; Bienert S; Haas J; Webb BM; Žídek A; Zheng W; Peisach E; Piehl DW; Anischanka I et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

GigaScience
2022-11-30 | Journal article
DOI: 10.1093/gigascience/giac118
Contributors: Mihaly Varadi; Sreenath Nair; Ian Sillitoe; Gerardo Tauriello; Stephen Anyango; Stefan Bienert; Clemente Borges; Mandar Deshpande; Tim Green; Demis Hassabis et al.
Source: check_circle
Crossref

The impact of AlphaFold Protein Structure Database on the fields of life sciences

PROTEOMICS
2022-11-16 | Journal article
DOI: 10.1002/pmic.202200128
Contributors: Mihaly Varadi; Sameer Velankar
Source: check_circle
Crossref

PDBe and PDBe‐KB: Providing high‐quality, up‐to‐date and integrated resources of macromolecular structures to support basic and applied research and education

Protein Science
2022-10 | Journal article
DOI: 10.1002/pro.4439
Contributors: Mihaly Varadi; Stephen Anyango; Sri Devan Appasamy; David Armstrong; Marcus Bage; John Berrisford; Preeti Choudhary; Damian Bertoni; Mandar Deshpande; Grisell Diaz Leines et al.
Source: check_circle
Crossref

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files

2022-08-13 | Preprint
DOI: 10.1101/2022.08.10.503473
Contributors: Preeti Choudhary; Stephen Anyango; John Berrisford; Mihaly Varadi; James Tolchard; Sameer Velankar
Source: check_circle
Crossref

Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology

International Journal of Molecular Sciences
2022-08-09 | Journal article
DOI: 10.3390/ijms23168877
Contributors: Hedvig Tordai; Erzsebet Suhajda; Ian Sillitoe; Sreenath Nair; Mihaly Varadi; Tamas Hegedus
Source: check_circle
Crossref
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3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

2022-08-03 | Preprint
DOI: 10.1101/2022.08.01.501973
Contributors: Mihaly Varadi; Sreenath Nair; Ian Sillitoe; Gerardo Tauriello; Stephen Anyango; Stefan Bienert; Clemente Borges; Mandar Deshpande; Tim Green; Demis Hassabis et al.
Source: check_circle
Crossref

PDB ProtVista: A reusable and open-source sequence feature viewer

2022-07-22 | Preprint
DOI: 10.1101/2022.07.22.500790
Contributors: Mandar Deshpande; Mihaly Varadi; Typhaine Paysan-Lafosse; Sreenath Nair; Damiano Piovesan; Saqib Mir; Aleksandras Gutmanas; Silvio C. E. Tosatto; Sameer Velankar
Source: check_circle
Crossref

Comprehensive collection and prediction of ABC transmembrane protein structures in the AI era of structural biology

2022-07-10 | Preprint
DOI: 10.1101/2022.07.08.499254
Contributors: Hedvig Tordai; Erzsébet Suhajda; Ian Sillitoe; Sreenath Nair; Mihály Váradi; Tamás Hegedűs
Source: check_circle
Crossref

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Nucleic Acids Research
2022-01-07 | Journal article
DOI: 10.1093/nar/gkab1061
Contributors: Mihaly Varadi; Stephen Anyango; Mandar Deshpande; Sreenath Nair; Cindy Natassia; Galabina Yordanova; David Yuan; Oana Stroe; Gemma Wood; Agata Laydon et al.
Source: check_circle
Crossref

PDBeCIF: an open-source mmCIF/CIF parsing and processing package

BMC Bioinformatics
2021-12 | Journal article
DOI: 10.1186/s12859-021-04271-9
Part of ISSN: 1471-2105
Source: Self-asserted source
Mihaly Varadi

PDBe-KB: collaboratively defining the biological context of structural data.

Nucleic acids research
2021-11 | Journal article
DOI: 10.1093/nar/gkab988
PMID: 34755867
Contributors: PDBe-KB consortium
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBe Aggregated API: Programmatic access to an integrative knowledge graph of molecular structure data.

Bioinformatics (Oxford, England)
2021-06 | Journal article
DOI: 10.1093/bioinformatics/btab424
PMID: 34081107
Contributors: Nair S; Váradi M; Nadzirin N; Pravda L; Anyango S; Mir S; Berrisford J; Armstrong D; Gutmanas A; Velankar S
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.

Briefings in bioinformatics
2021-03-01 | Journal article
DOI: 10.1093/bib/bbaa362
PMID: 33348379
PMC: PMC7799268
Source: Self-asserted source
Mihaly Varadi
grade
Preferred source (of 2)‎

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

Nucleic acids research
2021-01 | Journal article
DOI: 10.1093/nar/gkaa1021
PMID: 33305318
PMC: PMC7778965
Contributors: Lazar T; Martínez-Pérez E; Quaglia F; Hatos A; Chemes LB; Iserte JA; Méndez NA; Garrone NA; Saldaño TE; Marchetti J et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity

Scientific Reports
2020-04-01 | Journal article
DOI: 10.1038/s41598-020-62069-w
Contributors: Simone Kosol; Sara Contreras-Martos; Alessandro Piai; Mihaly Varadi; Tamas Lazar; Angela Bekesi; Pierre Lebrun; Isabella C. Felli; Roberta Pierattelli; Peter Tompa
Source: check_circle
Crossref

PDBe-KB Aggregated Views: Presenting PDB data in a different context

2019-12 | Other
DOI: 10.6019/tol.pdbe-kb-w.2019.00001.1
OTHER-ID:

C8038
Contributors: Pravda L; Varadi M
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBe: improved findability of macromolecular structure data in the PDB.

Nucleic acids research
2019-11 | Journal article
DOI: 10.1093/nar/gkz990
PMID: 31691821
Contributors: Armstrong DR; Berrisford JM; Conroy MJ; Gutmanas A; Anyango S; Choudhary P; Clark AR; Dana JM; Deshpande M; Dunlop R et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central

PDBe-KB: a community-driven resource for structural and functional annotations.

Nucleic acids research
2019-10-04 | Journal article
DOI: 10.1093/nar/gkz853
PMID: 31584092
Source: Self-asserted source
Mihaly Varadi

Protein Data Bank: the single global archive for 3D macromolecular structure data.

Nucleic acids research
2018-10 | Journal article
DOI: 10.1093/nar/gky949
PMID: 30357364
Contributors: wwPDB consortium
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
Preferred source (of 2)‎

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.

Nucleic acids research
2018-01 | Journal article
DOI: 10.1093/nar/gkx1070
PMID: 29126160
PMC: PMC5753225
Contributors: Mir S; Alhroub Y; Anyango S; Armstrong DR; Berrisford JM; Clark AR; Conroy MJ; Dana JM; Deshpande M; Gupta D et al.
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
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Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin.

2017 | Journal article
DOI: 10.1371/journal.pone.0174125
PMID: 28319173
Contributors: Nguyen HH; Varadi M; Tompa P; Pauwels K
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
Preferred source (of 2)‎

AmyPro: a database of proteins with validated amyloidogenic regions.

Nucleic acids research
2017-10 | Journal article
DOI: 10.1093/nar/gkx950
PMID: 29040693
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
Preferred source (of 2)‎

Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP

Scientific Reports
2017-07-05 | Journal article
DOI: 10.1038/s41598-017-04611-x
Contributors: Sara Contreras-Martos; Alessandro Piai; Simone Kosol; Mihaly Varadi; Angela Bekesi; Pierre Lebrun; Alexander N. Volkov; Kris Gevaert; Roberta Pierattelli; Isabella C. Felli et al.
Source: check_circle
Crossref
grade
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Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.

2016-01 | Journal article
DOI: 10.1016/j.bpj.2015.11.3516
PMID: 26789760
Contributors: Piai A; Calçada EO; Tarenzi T; Grande AD; Varadi M; Tompa P; Felli IC; Pierattelli R
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
Preferred source (of 2)‎

Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1185
PMID: 26582925
Contributors: Pancsa R; Varadi M; Tompa P; Vranken WF
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
Preferred source (of 2)‎

Computational approaches for inferring the functions of intrinsically disordered proteins.

2015 | Journal article
DOI: 10.3389/fmolb.2015.00045
PMID: 26301226
PMC: PMC4525029
Contributors: Varadi M; Vranken W; Guharoy M; Tompa P
Source: Self-asserted source
Mihaly Varadi via Europe PubMed Central
grade
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Peer review (1 review for 1 publication/grant)

Review activity for PloS one. (1)
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