MV
M. Varadi
Databases, ProteinbioinformaticsSoftwareProteinsComputational BiologyAlphaFoldPDBPDBx/mmCIFProtein ConformationProtein Folding
On Valency
published · living versionsW_53dcdcu2·v1 · currentpublished
Gaia Data Release 1: The variability processing & analysis and its application to the south ecliptic pole region
with L. Eyer, N. Mowlavi, D. W. Evans, K. Nienartowicz +68
1 version
Preprints & journals
44 papers in the corpus · 2003–2025AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities.40133787 · Fleming, Jennifer, Magana, Paulyna, Nair, Sreenath et al.2025 · 282 citationsJournal of molecular biology. 2025;437(15):168967
R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.39803519 · McCann, Holly, Meade, Caeden D, Williams, Loren Dean et al.2025 · 27 citationsbioRxiv : the preprint server for biology. 2024
Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit.39024028 · Bittrich, Sebastian, Midlik, Adam, Varadi, Mihaly et al.2024 · 7 citationsCurrent protocols. 2024;4(7):e1099
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank.38803272 · Choudhary, Preeti, Feng, Zukang, Berrisford, John et al.2024 · 17 citationsDatabase : the journal of biological databases and curation. 2024;2024
Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies.38774441 · Ellaway, Joseph I J, Anyango, Stephen, Nair, Sreenath et al.2026 · 26 citationsStructural dynamics (Melville, N.Y.). 2024;11(3):034701
Harnessing the 3D-Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data.38720559 · Magaña, Paulyna, Nair, Sreenath, Varadi, Mihaly et al.2024 · 1 citationCurrent protocols. 2024;4(5):e1047
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.37933859 · Varadi, Mihaly, Bertoni, Damian, Magana, Paulyna et al.2024 · 2,041 citationsNucleic acids research. 2024;52(D1):D368-D375
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2023.38015445 · Thakur, Matthew, Buniello, Annalisa, Brooksbank, Catherine et al.2024 · 33 citationsNucleic acids research. 2024;52(D1):D10-D17
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.38042830 · Kunnakkattu, Ibrahim Roshan, Choudhary, Preeti, Pravda, Lukas et al.2023 · 23 citationsJournal of cheminformatics. 2023;15(1):117
Annotating Macromolecular Complexes in the Protein Data Bank: Improving the FAIRness of Structure Data.38040737 · Appasamy, Sri Devan, Berrisford, John, Gaborova, Romana et al.2023 · 9 citationsScientific data. 2023;10(1):853
PDBImages: a command-line tool for automated macromolecular structure visualization.38085238 · Midlik, Adam, Nair, Sreenath, Anyango, Stephen et al.2023 · 0 citationsBioinformatics (Oxford, England). 2023;39(12)
Challenges in bridging the gap between protein structure prediction and functional interpretation.37850517 · Varadi, Mihaly, Tsenkov, Maxim, Velankar, Sameer2024 · 36 citationsProteins. 2025;93(1):400-410
Clustering predicted structures at the scale of the known protein universe.37704730 · Barrio-Hernandez, Inigo, Yeo, Jingi, Jänes, Jürgen et al.2023 · 361 citationsNature. 2023;622(7983):637-645
Identifying Protein Conformational States in the PDB and Comparison to AlphaFold2 Predictions10.1101/2023.07.13.545008v2 · Ellaway, J. I. J., Anyango, S., Nair, S. et al.2023 · 3 citationsbioRxiv
Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data.37045837 · Choudhary, Preeti, Anyango, Stephen, Berrisford, John et al.2023 · 10 citationsScientific data. 2023;10(1):204
ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.36828268 · Vallat, Brinda, Tauriello, Gerardo, Bienert, Stefan et al.2023 · 26 citationsJournal of molecular biology. 2023;435(14):168021
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.36807079 · Varadi, Mihaly, Bordin, Nicola, Orengo, Christine et al.2023 · 29 citationsCurrent opinion in structural biology. 2023;79:102543
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.36448847 · Varadi, Mihaly, Nair, Sreenath, Sillitoe, Ian et al.2022 · 31 citationsGigaScience. 2022;11
The impact of AlphaFold Protein Structure Database on the fields of life sciences.36382391 · Varadi, Mihaly, Velankar, Sameer2023 · 124 citationsProteomics. 2023;23(17):e2200128
PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.36173162 · Varadi, Mihaly, Anyango, Stephen, Appasamy, Sri Devan et al.2022 · 28 citationsProtein science : a publication of the Protein Society. 2022;31(10):e4439
Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files10.1101/2022.08.10.503473v1 · Choudhary, P., Anyango, S., Berrisford, J. et al.2022 · 2 citationsbioRxiv
Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology.36012140 · Tordai, Hedvig, Suhajda, Erzsebet, Sillitoe, Ian et al.2022 · 22 citationsInternational journal of molecular sciences. 2022;23(16)
PDB ProtVista: A reusable and open-source sequence feature viewer10.1101/2022.07.22.500790v2 · Deshpande, M., Varadi, M., Paysan-Lafosse, T. et al.2022 · 5 citationsbioRxiv
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.34791371 · Varadi, Mihaly, Anyango, Stephen, Deshpande, Mandar et al.2022 · 7,811 citationsNucleic acids research. 2022;50(D1):D439-D444
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.34081107 · Nair, Sreenath, Váradi, Mihály, Nadzirin, Nurul et al.2023 · 22 citationsBioinformatics (Oxford, England). 2021;37(21):3950-3952
PDBeCIF: an open-source mmCIF/CIF parsing and processing package.34301175 · van Ginkel, Glen, Pravda, Lukáš, Dana, José M et al.2021 · 12 citationsBMC bioinformatics. 2021;22(1):383
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.33348379 · Waman, Vaishali P, Sen, Neeladri, Varadi, Mihaly et al.2021 · 46 citationsBriefings in bioinformatics. 2021;22(2):742-768
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.33305318 · Lazar, Tamas, Martínez-Pérez, Elizabeth, Quaglia, Federica et al.2021 · 141 citationsNucleic acids research. 2021;49(D1):D404-D411
Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity.32238831 · Kosol, Simone, Contreras-Martos, Sara, Piai, Alessandro et al.2020 · 7 citationsScientific reports. 2020;10(1):5753
PDBe: improved findability of macromolecular structure data in the PDB.31691821 · Armstrong, David R, Berrisford, John M, Conroy, Matthew J et al.2020 · 210 citationsNucleic acids research. 2020;48(D1):D335-D343
AmyPro: a database of proteins with validated amyloidogenic regions.29040693 · Varadi, Mihaly, De Baets, Greet, Vranken, Wim F et al.2019 · 93 citationsNucleic acids research. 2018;46(D1):D387-D392
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.29126160 · Mir, Saqib, Alhroub, Younes, Anyango, Stephen et al.2019 · 83 citationsNucleic acids research. 2018;46(D1):D486-D492
Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.28680062 · Contreras-Martos, Sara, Piai, Alessandro, Kosol, Simone et al.2019 · 53 citationsScientific reports. 2017;7(1):4676
Affinity purification of human m-calpain through an intrinsically disordered inhibitor, calpastatin.28319173 · Nguyen, Hung Huy, Varadi, Mihaly, Tompa, Peter et al.2017 · 6 citationsPloS one. 2017;12(3):e0174125
Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy.26789760 · Piai, Alessandro, Calçada, Eduardo O, Tarenzi, Thomas et al.2016 · 41 citationsBiophysical journal. 2016;110(2):372-381
Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability.26582925 · Pancsa, Rita, Varadi, Mihaly, Tompa, Peter et al.2016 · 34 citationsNucleic acids research. 2016;44(D1):D429-34
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.26439842 · Varadi, Mihaly, Zsolyomi, Fruzsina, Guharoy, Mainak et al.2016 · 114 citationsPloS one. 2015;10(10):e0139731
Computational approaches for inferring the functions of intrinsically disordered proteins.26301226 · Varadi, Mihaly, Vranken, Wim, Guharoy, Mainak et al.2015 · 44 citationsFrontiers in molecular biosciences. 2015;2:45
DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder.25968230 · Varadi, Mihaly, Guharoy, Mainak, Zsolyomi, Fruzsina et al.2015 · 25 citationsBMC bioinformatics. 2015;16:153
The Protein Ensemble Database.26387108 · Varadi, Mihaly, Tompa, Peter2015 · 31 citationsAdvances in experimental medicine and biology. 2015;870:335-49
Predicting the predictive power of IDP ensembles.24507778 · Tompa, Peter, Varadi, Mihaly2014 · 20 citationsStructure (London, England : 1993). 2014;22(2):177-8
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins.24174539 · Varadi, Mihaly, Kosol, Simone, Lebrun, Pierre et al.2014 · 211 citationsNucleic acids research. 2014;42(Database issue):D326-35
Pulsational and evolutionary analysis of the double-mode RR Lyrae star BS Com0802.0135v1 · I. Dekany, G. Kovacs, J. Jurcsik et al.2008 · 6 citationsarXiv
A photometric monitoring of bright high-amplitude delta Scuti stars. II. Period updates for seven starsastro-ph/0303018v1 · A. Derekas, L.L. Kiss, P. Szekely et al.2003 · 18 citationsAstron.Astrophys. 402 (2003) 733-744
Career total: 62 works. 44 are in this corpus.
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