PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Open accessAbstract
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Databases of structural ensembles of proteins exist.
“Moreover, databases of structural ensembles of proteins exist264”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [264]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320 · see citing works
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698 · see citing works
CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 6,708 · see citing works
MolProbity: More and better reference data for improved all‐atom structure validation
Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., et al. (2018) · Protein Science · doi:10.1002/pro.3330 · Cited by 4,599 · see citing works
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1100 · Cited by 1,426 · see citing works
Self-citationPolymer physics of intracellular phase transitions
Brangwynne, C., Tompa, P., & Pappu, R. (2015) · Nature Physics · doi:10.1038/nphys3532 · Cited by 1,415 · see citing works
Self-citationIntrinsically Disordered Proteins in Human Diseases: Introducing the D 2 Concept
Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.125924 · Cited by 1,406 · see citing works
Structural Characterization of Flexible Proteins Using Small-Angle X-ray Scattering
Bernadó, P., Mylonas, E., Petoukhov, M. V., Blackledge, M. J., & Svergun, D. I. (2007) · Journal of the American Chemical Society · doi:10.1021/ja069124n · Cited by 1,172 · see citing works
Self-citationProtein Data Bank: the single global archive for 3D macromolecular structure data
wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky949 · Cited by 1,163 · see citing works
A series of PDB related databases for everyday needs
Joosten, R., Beek, T. T. T., Krieger, E., Hekkelman, M., Hooft, R., Schneider, R., Sander, C., & Vriend, G. (2010) · Nucleic Acids Res. · doi:10.1093/nar/gkq1105 · Cited by 1,050 · see citing works
Developing a molecular dynamics force field for both folded and disordered protein states
Robustelli, P., Piana, S., & Shaw, D. E. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800690115 · Cited by 1,047 · see citing works
A series of PDB-related databanks for everyday needs
Touw, W. G., Baakman, C. A. B., Black, J., Beek, T. A. H. T., Krieger, E., Joosten, R. P., & Vriend, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1028 · Cited by 936 · see citing works
Molecular interactions underlying liquid‐liquid phase separation of the FUS low‐complexity domain
Murthy, A. C., Dignon, G. L., Kan, Y., Zerze, G. H., Parekh, S. H., Mittal, J., & Fawzi, N. L. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0250-x · Cited by 698 · see citing works
Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering
Tria, G., Mertens, H. D. T., Kachala, M., & Svergun, D. I. (2015) · IUCrJ · doi:10.1107/s205225251500202x · Cited by 597 · see citing works
Self-citationHofmann, H., Soranno, A., Borgia, A., Gast, K., Nettels, D., & Schuler, B. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207719109 · Cited by 480 · see citing works
Allostery in Its Many Disguises: From Theory to Applications
Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., et al. (2019) · Structure · doi:10.1016/j.str.2019.01.003 · Cited by 404 · see citing works
Structure and Function of Intrinsically Disordered Proteins
Tompa, P., & Fersht, A. (2009) · Chapman & Hall/CRC eBooks · doi:10.1201/9781420078930 · Cited by 330 · see citing works
Self-citationJensen, M. R., Zweckstetter, M., Huang, J., & Blackledge, M. J. (2014) · Chemical Reviews · doi:10.1021/cr400688u · Cited by 298 · see citing works
Self-citationSASBDB: Towards an automatically curated and validated repository for biological scattering data
Kikhney, A., Borges, C., Molodenskiy, D. S., Jeffries, C. M., & Svergun, D. I. (2019) · Protein Science · doi:10.1002/pro.3731 · Cited by 262 · see citing works
Self-citationDisProt: intrinsic protein disorder annotation in 2020
Hatos, A., Hajdu-Soltész, B., Monzón, A. M., Palópoli, N., Álvarez, L., Fas, B. A., Bassot, C., Benítez, G. I., Bevilacqua, M., Chasapi, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz975 · Cited by 224 · see citing works
Self-citationJakob, U., Kriwacki, R. W., & Uversky, V. N. (2014) · Chemical Reviews · doi:10.1021/cr400459c · Cited by 216 · see citing works
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
Váradi, M., Kosol, S., Lebrun, P., Valentini, E., Blackledge, M. J., Dunker, A. K., Felli, I. C., Forman-Kay, J. D., Kriwacki, R. W., Pierattelli, R., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt960 · Cited by 211 · see citing works
Self-citationPiovesan, D., Tabaro, F., Paladin, L., Necci, M., Mičetić, I., Camilloni, C., Davey, N. E., Dosztányi, Z., Mészáros, B., Monzón, A. M., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1071 · Cited by 208 · see citing works
Self-citationStructural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy
Kosol, S., Contreras-Martos, S., Cedeño, C., & Tompa, P. (2013) · Molecules · doi:10.3390/molecules180910802 · Cited by 199 · see citing works
Self-citationSong, D., Luo, R., & Chen, H. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00135 · Cited by 198 · see citing works
Fuertes, G., Banterle, N., Ruff, K. M., Chowdhury, A., Mercadante, D., Koehler, C., Kachala, M., Girona, G. E., Milles, S., Mishra, A., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1704692114 · Cited by 198 · see citing works
Self-citationSchwalbe, M., Ozenne, V., Bibow, S., Jaremko, M., Jaremko, Ł., Gajda, M. J., Jensen, M. R., Biernat, J., Becker, S., Mandelkow�, E., et al. (2013) · Structure · doi:10.1016/j.str.2013.10.020 · Cited by 192 · see citing works
Self-citationMol*: Towards a Common Library and Tools for Web Molecular Graphics
Sehnal, D., Rose, A., Koča, J., Burley, S. K., & Velankar, S. S. (2018) · Eurographics · doi:10.2312/molva.20181103 · Cited by 158 · see citing works
Interactions by disorder – A matter of context
Bugge, K., Brakti, I., Fernandes, C. B., Dreier, J. E., Lundsgaard, J. E., Olsen, J. G., Skriver, K., & Kragelund, B. B. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00110 · Cited by 155 · cited 1× · see citing works
“However, this recent abundance of LDRs is predominantly due to the context-dependent folding of proteins with conditional disorder, such as pH sensitivity, PTM-dependent folding, localization-dependent disorder and folding upon binding to a partner (7–9).”
BackgroundCharacterization of disordered proteins with ENSEMBLE
Krzeminski, M., Marsh, J. A., Neale, C., Choy, W., & Forman-Kay, J. D. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts701 · Cited by 154 · see citing works
Self-citationCATH: expanding the horizons of structure-based functional annotations for genome sequences
Sillitoe, I., Dawson, N., Lewis, T. E., Das, S., Lees, J., Ashford, P., Tolulope, A., Scholes, H. M., Senatorov, I. S., Bujan, A., et al. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1097 · Cited by 147 · see citing works
The (un)structural biology of biomolecular liquid-liquid phase separation using NMR spectroscopy
Murthy, A. C., & Fawzi, N. L. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.009847 · Cited by 135 · see citing works
Targeting intrinsically disordered proteins at the edge of chaos
Ruan, H., Sun, Q., Zhang, W., Liu, Y., & Lai, L. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2018.09.017 · Cited by 133 · see citing works
Mapping the Potential Energy Landscape of Intrinsically Disordered Proteins at Amino Acid Resolution
Ozenne, V., Schneider, R. C., Yao, M., Huang, J., Salmon, L., Zweckstetter, M., Jensen, M. R., & Blackledge, M. J. (2012) · Journal of the American Chemical Society · doi:10.1021/ja306905s · Cited by 129 · see citing works
Self-citationPDBe-KB: a community-driven resource for structural and functional annotations
Váradi, M., Berrisford, J. M., Deshpande, M., Nair, S. S., Gutmanas, A., Armstrong, D. R., Pravda, L., Al‐Lazikani, B., Anyango, S., Barton, G. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz853 · Cited by 124 · see citing works
Self-citationSimultaneous quantification of protein order and disorder
Sormanni, P., Piovesan, D., Heller, G. T., Bonomi, M., Kukić, P., Camilloni, C., Fuxreiter, M., Dosztányi, Z., Pappu, R. V., Babu, M. M., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2331 · Cited by 118 · see citing works
Self-citationTargeting Intrinsically Disordered Transcription Factors: Changing the Paradigm
Tsafou, K., Tiwari, P. B., Forman-Kay, J. D., Metallo, S. J., & Toretsky, J. A. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.04.008 · Cited by 110 · see citing works
Self-citationStructural Modeling Using Solution Small-Angle X-ray Scattering (SAXS)
Gräwert, T., & Svergun, D. I. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.01.030 · Cited by 108 · see citing works
Self-citationTompa, P. (2013) · Chemical Reviews · doi:10.1021/cr4005082 · Cited by 101 · see citing works
Self-citationShrestha, U. R., Juneja, P., Zhang, Q., Gurumoorthy, V., Borreguero, J. M., Urban, V. S., Cheng, X., Pingali, S. V., Smith, J. C., O’Neill, H., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907251116 · Cited by 101 · see citing works
Efficient Ensemble Refinement by Reweighting
Köfinger, J., Stelzl, L. S., Reuter, K., Allande, C., Reichel, K., & Hummer, G. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b01231 · Cited by 94 · see citing works
SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
Nagy, G., Igaev, M., Jones, N. C., Hoffmann, S. V., & Grubmüller, H. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00203 · Cited by 94 · see citing works
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins
Schád, É., Fichó, E., Pancsa, R., Simon, I., Dosztányi, Z., & Mészáros, B. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx640 · Cited by 93 · see citing works
Computer Simulations of Intrinsically Disordered Proteins
Chong, S., Chatterjee, P., & Ham, S. (2017) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-052516-050843 · Cited by 84 · see citing works
Small-angle scattering studies of intrinsically disordered proteins and their complexes
Cordeiro, T. N., Herranz-Trillo, F., Urbanek, A., Estaña, A., Cortés, J., Sibille, N., & Bernadó, P. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.10.011 · Cited by 84 · see citing works
Self-citationDelaforge, E., Kragelj, J., Tengo, L., Palencia, A., Milles, S., Bouvignies, G., Salvi, N., Blackledge, M. J., & Jensen, M. R. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b12407 · Cited by 80 · see citing works
Self-citationComparison and Evaluation of Force Fields for Intrinsically Disordered Proteins
Rahman, M. U., Rehman, A. U., Liu, H., & Chen, H. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00762 · Cited by 74 · see citing works
Determination of Structural Ensembles of Proteins: Restraining vs Reweighting
Rangan, R., Bonomi, M., Heller, G. T., Cesari, A., Bussi, G., & Vendruscolo, M. (2018) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b00738 · Cited by 72 · see citing works
Sterckx, Y. G. ‐., Volkov, A. N., Vranken, W., Kragelj, J., Jensen, M. R., Buts, L., Garcia‐Pino, A., Jové, T., Melderen, L. V., Blackledge, M. J., et al. (2014) · Structure · doi:10.1016/j.str.2014.03.012 · Cited by 70 · see citing works
Self-citationMFIB: a repository of protein complexes with mutual folding induced by binding
Fichó, E., Reményi, I., Simon, I., & Mészáros, B. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx486 · Cited by 70 · see citing works
Holmstrom, E. D., Holla, A., Zheng, W., Nettels, D., Best, R. B., & Schuler, B. (2018) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2018.09.030 · Cited by 68 · see citing works
BioMagResBank (BMRB) as a Resource for Structural Biology
Romero, P. R., Kobayashi, N., Wedell, J. R., Baskaran, K., Iwata, T., Yokochi, M., Maziuk, D., Yao, H., Fujiwara, T., Kurisu, G., et al. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0270-6_14 · Cited by 67 · see citing works
Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins
Hamdi, K., Salladini, E., O'Brien, D. P., Brier, S., Chenal, A., Yacoubi, I., & Longhi, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-15299-4 · Cited by 62 · see citing works
Self-citationVallet, S. D., Miele, A. E., Uciechowska‐Kaczmarzyk, U., Liwo, A., Duclos, B., Samsonov, S. A., & Ricard‐Blum, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-30190-6 · Cited by 53 · see citing works
Self-citationMonzón, A. M., Necci, M., Quaglia, F., Walsh, I., Piovesan, D., Zanotti, G., & Tosatto, S. C. E. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21124496 · Cited by 35 · see citing works
Self-citationDistance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins
Lázár, T., Guharoy, M., Vranken, W., Rauscher, S., Wodak, S. J., & Tompa, P. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.05.015 · Cited by 34 · see citing works
Self-citationThe Feature-Viewer: a visualization tool for positional annotations on a sequence
Paladin, L., Schaeffer, M., Gaudet, P., Zahn‐Zabal, M., Michel, P.-A., Piovesan, D., Tosatto, S. C. E., & Bairoch, A. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa055 · Cited by 30 · see citing works
Self-citationAn intrinsically disordered proteins community for ELIXIR
Davey, N. E., Babu, M. M., Blackledge, M. J., Bridge, A. J., Capella-Gutiérrez, S., Dosztányi, Z., Drysdale, R. A., Edwards, R. J., Elofsson, A., Felli, I. C., et al. (2019) · F1000Research · doi:10.12688/f1000research.20136.1 · Cited by 20 · see citing works
Self-citationConditionally disordered proteins: bringing the environment back into the fold
Hausrath, A. C., & Kingston, R. L. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2558-1 · Cited by 17 · see citing works
Modeling Resilience to Damage in Multiple Sclerosis: Plasticity Meets Connectivity
Bassi, M. S., Iezzi, E., Pavone, L., Mandolesi, G., Musella, A., Gentile, A., Gilio, L., Centonze, D., & Buttari, F. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010143 · Cited by 17 · see citing works
Salvi, N., Salmon, L., & Blackledge, M. J. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b01566 · Cited by 14 · see citing works
Self-citationde Opakua, A. I., Merino, N., Villate, M., Cordeiro, T. N., Ormaza, G., Sänchez‐Carbayo, M., Diercks, T., Bernadó, P., & Blanco, F. J. (2017) · PLoS ONE · doi:10.1371/journal.pone.0172507 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
3 of the 65 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
Sehnal, D., Bittrich, S., Deshpande, M., Svobodová, R., Berka, K., Bazgier, V., Velankar, S., Burley, S. K., Koča, J., & Rose, A. S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab314 · Cited by 1,154 · see citing works
The molecular basis for cellular function of intrinsically disordered protein regions
Holehouse, A. S., & Kragelund, B. B. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00673-0 · Cited by 717 · see citing works
AlphaFold and Implications for Intrinsically Disordered Proteins
Ruff, K. M., & Pappu, R. V. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167208 · Cited by 635 · see citing works
Self-citationSystematic identification of conditionally folded intrinsically disordered regions by AlphaFold2
Alderson, T. R., Pritišanac, I., Kolarić, Đ., Moses, A. M., & Forman-Kay, J. D. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2304302120 · Cited by 240 · see citing works
Self-citationDirect prediction of intrinsically disordered protein conformational properties from sequence
Lotthammer, J. M., Ginell, G. M., Griffith, D., Emenecker, R. J., & Holehouse, A. S. (2024) · Nature Methods · doi:10.1038/s41592-023-02159-5 · Cited by 228 · see citing works
Brocca, S., Grandori, R., Longhi, S., & Uversky, V. N. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21239045 · Cited by 189 · see citing works
Self-citationDisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
Quaglia, F., Mészáros, B., Salladini, E., Hatos, A., Pancsa, R., Chemes, L. B., Pajkos, M., Lázár, T., Peña‐Díaz, S., Santos, J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1082 · Cited by 157 · see citing works
Self-citationHatos, A., Tosatto, S. C. E., Vendruscolo, M., & Fuxreiter, M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac386 · Cited by 158 · see citing works
Self-citationMobiDB: 10 years of intrinsically disordered proteins
Piovesan, D., Conte, A. D., Clementel, D., Monzón, A. M., Bevilacqua, M., Aspromonte, M. C., Iserte, J., Orti, F., Marino‐Buslje, C., & Tosatto, S. C. E. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1065 · Cited by 158 · see citing works
Self-citationDisProt in 2024: improving function annotation of intrinsically disordered proteins
Aspromonte, M. C., Nugnes, M. V., Quaglia, F., Bouharoua, A., Sagris, V., Promponas, V. J., Chasapi, A., Fichó, E., Balatti, G. E., Parisi, G. D., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad928 · Cited by 142 · see citing works
Self-citationThe structural context of posttranslational modifications at a proteome-wide scale
Bludau, I., Willems, S., Zeng, W., Strauss, M. T., Hansen, F. M., Tanzer, M. C., Karayel, Ö., Schulman, B. A., & Mann, M. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001636 · Cited by 119 · see citing works
AlphaFold prediction of structural ensembles of disordered proteins
Brotzakis, Z. F., Zhang, S., Murtada, M. H., & Vendruscolo, M. (2025) · Nature Communications · doi:10.1038/s41467-025-56572-9 · Cited by 99 · see citing works
Zhu, J., Salvatella, X., & Robustelli, P. (2022) · Nature Communications · doi:10.1038/s41467-022-34077-z · Cited by 92 · see citing works
<scp>DSSP</scp> 4: <scp>FAIR</scp> annotation of protein secondary structure
Hekkelman, M. L., Salmoral, D. Á., Perrakis, A., & Joosten, R. P. (2025) · Protein Science · doi:10.1002/pro.70208 · Cited by 97 · see citing works
Lindorff-Larsen, K., & Kragelund, B. B. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167196 · Cited by 85 · see citing works
Zeng, X., Ruff, K. M., & Pappu, R. V. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2200559119 · Cited by 71 · see citing works
Self-citationGhafouri, H., Lázár, T., Conte, A. D., Tenorio, L., Aspromonte, M. C., Bernadó, P., Chaves‐Arquero, B., Chemes, L. B., Clementel, D., Cordeiro, T. N., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad947 · Cited by 71 · see citing works
Self-citationComputer-Aided Drug Discovery for Undruggable Targets
Sun, Q., Wang, H., Xie, J., Wang, L., Mu, J., Li, J., Ren, Y., & Lai, L. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00969 · Cited by 69 · see citing works
Design of intrinsically disordered protein variants with diverse structural properties
Pesce, F., Bremer, A., Tesei, G., Hopkins, J. B., Grace, C. R., Mittag, T., & Lindorff-Larsen, K. (2024) · Science Advances · doi:10.1126/sciadv.adm9926 · Cited by 60 · see citing works
Self-citationMaiti, S., Singh, A., Maji, T., Saibo, N. V., & De, S. (2024) · Current Research in Structural Biology · doi:10.1016/j.crstbi.2024.100138 · Cited by 61 · see citing works
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection
Rigden, D. J., & Fernández, X. M. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1216 · Cited by 59 · see citing works
Rules of Physical Mathematics Govern Intrinsically Disordered Proteins
Ghosh, K., Huihui, J., Phillips, M. W., & Haider, A. (2022) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-120221-095357 · Cited by 57 · see citing works
FuzDB: a new phase in understanding fuzzy interactions
Hatos, A., Monzón, A. M., Tosatto, S. C. E., Piovesan, D., & Fuxreiter, M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1060 · Cited by 54 · see citing works
Self-citationECO: the Evidence and Conclusion Ontology, an update for 2022
Nadendla, S., Jackson, R., Munro, J. B., Quaglia, F., Mészáros, B., Olley, D., Hobbs, E., Goralski, S. M., Chibucos, M. C., Mungall, C., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1025 · Cited by 51 · see citing works
Self-citationAdvancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
Duran-Frigola, M., Cigler, M., & Winter, G. E. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c11098 · Cited by 50 · see citing works
Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma
Kulkarni, P., Leite, V. B. P., Roy, S., Bhattacharyya, S., Mohanty, A. R., Achuthan, S., Singh, D., Appadurai, R., Govindan Rangarajan, C., Weninger, K., et al. (2022) · Biophysics Reviews · doi:10.1063/5.0080512 · Cited by 50 · see citing works
Molecular grammars of predicted intrinsically disordered regions that span the human proteome
Ruff, K. M., King, M. R., Ying, A. W., Liu, V., Pant, A., Lieberman, W. E., Shinn, M. K., Su, X., Kadoch, C., & Pappu, R. V. (2025) · Cell · doi:10.1016/j.cell.2025.10.019 · Cited by 57 · see citing works
Self-citationRational drug design targeting intrinsically disordered proteins
Wang, H., Xiong, R., & Lai, L. (2023) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1685 · Cited by 39 · see citing works
Challenges in bridging the gap between protein structure prediction and functional interpretation
Varadi, M., Tsenkov, M., & Velankar, S. (2025) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26614 · Cited by 36 · see citing works
Compositional Bias of Intrinsically Disordered Proteins and Regions and Their Predictions
Zhao, B., & Kurgan, L. (2022) · Biomolecules · doi:10.3390/biom12070888 · Cited by 36 · see citing works
EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023
Thakur, M., Buniello, A., Brooksbank, C., Gurwitz, K. T., Hall, M. D., Hartley, M., Hulcoop, D. G., Leach, A. R., Marquês, D., Martin, M. J., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1088 · Cited by 33 · see citing works
A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis
Tempra, C., Scollo, F., Pannuzzo, M., Lolicato, F., & Rosa, C. L. (2022) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2022.140767 · Cited by 32 · see citing works
Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience · doi:10.1093/gigascience/giac118 · Cited by 32 · see citing works
Self-citationRóżycki, B., & Bouřa, E. (2022) · Biophysical Chemistry · doi:10.1016/j.bpc.2022.106843 · Cited by 31 · see citing works
Liu, J., Liu, J., Deng, L., Liu, H., Liu, H., Zhao, W., Zhao, Y., Sun, X., Fan, S., Wang, H., et al. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad074 · Cited by 31 · see citing works
Jones, M. S., Shmilovich, K., & Ferguson, A. L. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00840 · Cited by 29 · see citing works
Advanced computational approaches to understand protein aggregation
Ghosh, D., Biswas, A., & Radhakrishna, M. (2024) · Biophysics Reviews · doi:10.1063/5.0180691 · Cited by 31 · see citing works
Clerc, I., Sagar, A., Barducci, A., Sibille, N., Bernadó, P., & Cortés, J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.06.031 · Cited by 29 · see citing works
Self-citationSalladini, E., Gondelaud, F., Nilsson, J. F., Pesce, G., Bignon, C., Murrali, M. G., Fabre, R., Pierattelli, R., Kajava, A. V., Horvat, B., et al. (2021) · Biomolecules · doi:10.3390/biom11091324 · Cited by 30 · see citing works
Self-citationZhu, J., Li, Z., Zhang, B., Zheng, Z., Zhong, B., Bai, J., Hong, X., Wang, T., Wei, T., Yang, J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.05.592611 · Cited by 31 · see citing works
Schiavina, M., Salladini, E., Murrali, M. G., Tria, G., Felli, I. C., Pierattelli, R., & Longhi, S. (2020) · Scientific Reports · doi:10.1038/s41598-020-76522-3 · Cited by 27 · see citing works
Self-citationConformational landscape of multidomain SMAD proteins
Gomes, T., Martín-Malpartida, P., Ruiz, L., Aragón, E., Cordeiro, T. N., & Macías, M. J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.09.009 · Cited by 25 · see citing works
Self-citationHatos, A., Teixeira, J. M. C., Barrera-Vilarmau, S., Horváth, A., Tosatto, S. C. E., Vendruscolo, M., & Fuxreiter, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad214 · Cited by 24 · see citing works
Self-citationAtomic resolution ensembles of intrinsically disordered proteins with Alphafold
Schnapka, V., Morozova, T. I., Sen, S., & Bonomi, M. (2026) · Nature Communications · doi:10.1038/s41467-026-69172-y · Cited by 23 · see citing works
Conformations, interactions and functions of intrinsically disordered syndecans
Ricard‐Blum, S., & Couchman, J. (2023) · Biochemical Society Transactions · doi:10.1042/bst20221085 · Cited by 22 · see citing works
Self-citationAlphaFold Prediction of Structural Ensembles of Disordered Proteins
Brotzakis, Z. F., Zhang, S., & Vendruscolo, M. (2023) · doi:10.1101/2023.01.19.524720 · Cited by 22 · see citing works
Antila, H., Kav, B., Miettinen, M. S., Martinez‐Seara, H., Jungwirth, P., & Ollila, O. H. S. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c01954 · Cited by 21 · see citing works
Data science techniques in biomolecular force field development
Ding, Y., Yu, K., & Huang, J. (2022) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2022.102502 · Cited by 21 · see citing works
Tesei, G., Trolle, A. I., Jonsson, N., Betz, J., Pesce, F., Johansson, K. E., & Lindorff‐Larsen, K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.08.539815 · Cited by 21 · see citing works
Kjærgaard, M. (2022) · Biochemistry · doi:10.1021/acs.biochem.1c00737 · Cited by 20 · see citing works
Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses
Gondelaud, F., Pesce, G., Nilsson, J. F., Bignon, C., Ptchelkine, D., Gerlier, D., Mathieu, C., & Longhi, S. (2022) · Essays in Biochemistry · doi:10.1042/ebc20220045 · Cited by 20 · see citing works
Self-citationZhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2025) · Communications Biology · doi:10.1038/s42003-025-08783-5 · Cited by 19 · see citing works
Martin, W., Sheynkman, G., Lightstone, F. C., Nussinov, R., & Cheng, F. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.09.001 · Cited by 18 · see citing works
Artificial neural networks for solution scattering data analysis
Molodenskiy, D. S., Svergun, D. I., & Kikhney, A. (2022) · Structure · doi:10.1016/j.str.2022.03.011 · Cited by 18 · see citing works
Self-citationMészáros, B., Hatos, A., Palópoli, N., Quaglia, F., Salladini, E., Roey, K. V., Arthanari, H., Dosztányi, Z., Felli, I. C., Fischer, P. D., et al. (2023) · Nature Methods · doi:10.1038/s41592-023-01915-x · Cited by 18 · see citing works
Self-citation(2023) · doi:10.1093/bioinformatics/btad739 · Cited by 18 · see citing works
Self-citationFunctions of intrinsically disordered proteins through evolutionary lenses
Pajkos, M., & Dosztányi, Z. (2021) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2021.06.017 · Cited by 18 · see citing works
Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide‐Activated Sirtuin 7**
Bolding, J. E., Nielsen, A. L., Jensen, I., Hansen, T. N., Ryberg, L. A., Jameson, S. T., Harris, P., Peters, G. H. J., Denu, J. M., Rogers, J. M., et al. (2023) · Angewandte Chemie International Edition · doi:10.1002/anie.202314597 · Cited by 17 · see citing works
Accurate Generation of Conformational Ensembles for Intrinsically Disordered Proteins with IDPFold
Zhu, J., Li, Z., Zheng, Z., Zhang, B., Zhong, B., Bai, J., Hong, X., Wang, T., Wei, T., Yang, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202511636 · Cited by 18 · see citing works
Databases for intrinsically disordered proteins
Piovesan, D., Monzón, A. M., Quaglia, F., & Tosatto, S. C. E. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798321012109 · Cited by 16 · see citing works
Self-citationThe Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins
Paladino, A., Vitagliano, L., & Graziano, G. (2023) · Biology · doi:10.3390/biology12050754 · Cited by 16 · see citing works
Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles
Viegas, R. G., Martins, I. B. S., & Leite, V. B. P. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00080 · Cited by 16 · see citing works
Harmat, Z., Dudola, D., & Gáspári, Z. (2021) · Biomolecules · doi:10.3390/biom11101505 · Cited by 15 · see citing works
Intrinsic disorder and flexibility in proteins: a challenge for structural biology and drug design
Zanotti, G. (2023) · Crystallography Reviews · doi:10.1080/0889311x.2023.2208518 · Cited by 15 · see citing works
Integrative ensemble modeling of proteins and their complexes with distance distribution restraints
Jeschke, G., & Hofer, L. E. (2022) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2022.02.010 · Cited by 15 · see citing works
The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection
Vieira, M. F. M., Hernandez, G., Zhong, Q., Arbesú, M., Veloso, T., Gomes, T., Martins, M. L., Monteiro, H., Frazão, C., Frankel, G., et al. (2024) · Communications Biology · doi:10.1038/s42003-024-05856-9 · Cited by 14 · see citing works
Self-citationHybrid computational methods combining experimental information with molecular dynamics
Mondal, A., Lenz, S., MacCallum, J. L., & Pérez, A. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102609 · Cited by 14 · see citing works
Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans
Gondelaud, F., Bouakil, M., Fèvre, A. L., Miele, A. E., Chirot, F., Duclos, B., Liwo, A., & Ricard‐Blum, S. (2021) · Matrix Biology Plus · doi:10.1016/j.mbplus.2021.100081 · Cited by 14 · see citing works
Self-citationMészáros, B., Park, E., Malinverni, D., Sejdiu, B. I., Immadisetty, K., Sandhu, M., Lang, B., & Babu, M. M. (2023) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102608 · Cited by 13 · see citing works
Protein ensemble modeling and analysis with MMMx
Jeschke, G. (2024) · Protein Science · doi:10.1002/pro.4906 · Cited by 12 · see citing works
Experimental Evidence of Intrinsic Disorder and Amyloid Formation by the Henipavirus W Proteins
Pesce, G., Gondelaud, F., Ptchelkine, D., Nilsson, J. F., Bignon, C., Cartalas, J., Fourquet, P., & Longhi, S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23020923 · Cited by 13 · see citing works
Self-citationJeschke, G. (2022) · Biomolecules · doi:10.3390/biom12101369 · Cited by 13 · see citing works
Integrative Conformational Ensembles of Sic1 Using Different Initial Pools and Optimization Methods
Gomes, G.-N. W., Namini, A., & Gradinaru, C. C. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.910956 · Cited by 12 · see citing works
Self-citationSUMO1 hinders α‐Synuclein fibrillation by inducing structural compaction
Panigrahi, R., Krishnan, R., Singh, J., Padinhateeri, R., & Kumar, A. (2023) · Protein Science · doi:10.1002/pro.4632 · Cited by 12 · see citing works
Calculating Pairwise Similarity of Polymer Ensembles via Earth Mover’s Distance
Shi, J., Walsh, D. J., Zou, W., Rebello, N., Deagen, M. E., Fransen, K. A., Gao, X., Olsen, B. D., & Audus, D. J. (2024) · ACS Polymers Au · doi:10.1021/acspolymersau.3c00029 · Cited by 11 · see citing works
Comprehensive folding variations for protein folding
Yang, J., Cheng, W. X., Zhao, X. F., Wu, G., Sheng, S. T., Hu, Q., Ge, H., Qin, Q., Jin, X., Zhang, L., et al. (2022) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26381 · Cited by 11 · see citing works
Condeminas, M., & Macías, M. J. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2023.102764 · Cited by 10 · see citing works
More is simpler: Decomposition of ligand‐binding affinity for proteins being disordered
Wang, X., Chong, B., Sun, Z., Ruan, H., Yang, Y., Song, P., & Liu, Z. (2022) · Protein Science · doi:10.1002/pro.4375 · Cited by 10 · see citing works
Predicting Protein Conformational Disorder and Disordered Binding Sites
Tamburrini, K. C., Pesce, G., Nilsson, J. F., Gondelaud, F., Kajava, A. V., Berrin, J., & Longhi, S. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2095-3_4 · Cited by 10 · see citing works
Self-citationSun, B., & Kekenes-Huskey, P. M. (2023) · Quarterly Reviews of Biophysics · doi:10.1017/s003358352300001x · Cited by 9 · see citing works
Intrinsically disordered proteins at the nano-scale
Ehm, T., Shinar, H., Meir, S., Sekhon, A., Sethi, V., Morgan, I. L., Rahamim, G., Saleh, O. A., & Beck, R. (2021) · Nano Futures · doi:10.1088/2399-1984/abfb7c · Cited by 8 · see citing works
When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes
Sacquin‐Mora, S., & Prévost, C. (2021) · Biomolecules · doi:10.3390/biom11101529 · Cited by 8 · see citing works
Exploiting Bioschemas Markup to Populate IDPcentralPreprint
Gray, A. J. G., Papadopoulos, P., Mičetić, I., & Hatos, A. (2021) · doi:10.37044/osf.io/v3jct · Cited by 8 · see citing works
Self-citationBonneau, K., Pasos-Trejo, A. S., Plainer, M., Sagresti, L., Venturin, J., Zaporozhets, I., Caruso, A., Rolando, E., Guljas, A., Klein, L., et al. (2026) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.70064 · Cited by 7 · see citing works
Sureshan, M., Brintha, S., & Jothi, A. (2023) · Molecular Diversity · doi:10.1007/s11030-023-10679-7 · Cited by 7 · see citing works
A curated rotamer library for common post-translational modifications of proteins
Zhang, O., Naik, S. A., Liu, Z. H., Forman-Kay, J. D., & Head-Gordon, T. L. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae444 · Cited by 7 · see citing works
Self-citationLoCoHD: a metric for comparing local environments of proteins
Fazekas, Z., Menyhárd, D. K., & Perczel, A. (2024) · Nature Communications · doi:10.1038/s41467-024-48225-0 · Cited by 7 · see citing works
Zheng, W., Du, Z., Ko, S. B., Wickramasinghe, N. P., & Yang, S. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c05456 · Cited by 7 · see citing works
PROTHON: A Local Order Parameter-Based Method for Efficient Comparison of Protein Ensembles
Aina, A., Hsueh, S. C. C., & Plotkin, S. S. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00145 · Cited by 7 · see citing works
Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering
Tsangaris, T. E., Smyth, S., Gomes, G.-N. W., Liu, Z. H., Milchberg, M. H., Bah, A., Wasney, G. A., Forman-Kay, J. D., & Gradinaru, C. C. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c04052 · Cited by 7 · see citing works
Self-citationStructural plasticity of the FOXO-DBD:p53-TAD interaction
Kohoutová, K., Srb, P., Obšilová, V., Veverka, V., & Obšil, T. (2025) · Nature Communications · doi:10.1038/s41467-025-59106-5 · Cited by 6 · see citing works
Intrinsically disordered proteins and liquid–liquid phase separation in drug discovery
Deka, N., Nag, N., & Tripathi, T. (2026) · Drug Discovery Today · doi:10.1016/j.drudis.2026.104603 · Cited by 7 · see citing works
Low-resolution description of the conformational space for intrinsically disordered proteins
Förster, G. D., Idier, J., Liberti, L., Mucherino, A., Lin, J., & Malliavin, T. E. (2022) · Scientific Reports · doi:10.1038/s41598-022-21648-9 · Cited by 6 · see citing works
Angioletti, D., Raniolo, S., & Limongelli, V. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0280330 · Cited by 6 · see citing works
Saibo, N. V., Maiti, S., Acharya, B., & De, S. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90264-9.00032-5 · Cited by 6 · see citing works
Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau
Maiti, S., & Heyden, M. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c01726 · Cited by 5 · see citing works
Bastida, A., Zúñiga, J., Fogolari, F., & Soler, M. A. (2024) · Physical Chemistry Chemical Physics · doi:10.1039/d4cp02564d · Cited by 5 · see citing works
Interpreting Transient Interactions of Intrinsically Disordered Proteins
Wohl, S., & Zheng, W. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c00096 · Cited by 5 · see citing works
Pesce, G., Gondelaud, F., Ptchelkine, D., Bignon, C., Fourquet, P., & Longhi, S. (2024) · FEBS Journal · doi:10.1111/febs.17239 · Cited by 5 · see citing works
Self-citation
- Authors
- Lazar, T., Martínez-Pérez, E., Quaglia, F., Hatos, A., Chemes, L. B., Iserte, J. A., Méndez, N. A., Garrone, N. A., Saldaño, T. E., Marchetti, J., Rueda, A. J. V., Bernadó, P., Blackledge, M., Cordeiro, T. N., Fagerberg, E., Forman-Kay, J. D., Fornasari, M. S., Gibson, T. J., Gomes, G.-N. W., Gradinaru, C. C., Head-Gordon, T., Jensen, M. R., Lemke, E. A., Longhi, S., Marino-Buslje, C., Minervini, G., Mittag, T., Monzon, A. M., Pappu, R. V., Parisi, G., Ricard-Blum, S., Ruff, K. M., Salladini, E., Skepö, M., Svergun, D., Vallet, S. D., Varadi, M., Tompa, P., Tosatto, S. C. E., & Piovesan, D.
- Affiliations
- VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina
- University of Padua (IT)
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde’’, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina
- Fundación Instituto Leloir (AR)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- National University of Quilmes (AR)
- Centre National de la Recherche Scientifique (FR)
- Lund University (SE)
- University of Toronto (CA)
- Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina
- European Molecular Biology Laboratory (DE)
- University of California, Berkeley (US)
- Johannes Gutenberg University Mainz (DE)
- St. Jude Children's Research Hospital (US)
- Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy
- Washington University in St. Louis (US)
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France
- Lyon 1 Université (FR)
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Corresponding author
- Tosatto, Silvio C E
- ORCID
- Lazar, Tamas
- Martínez-Pérez, Elizabeth
- Quaglia, Federica
- Hatos, András
- Chemes, Lucía B
- Iserte, Javier A
- Méndez, Nicolás A
- Garrone, Nicolás A
- Saldaño, Tadeo E
- Marchetti, Julia
- Rueda, Ana Julia Velez
- Bernadó, Pau
- Blackledge, Martin
- Cordeiro, Tiago N
- Fagerberg, Eric
- Forman-Kay, Julie D
- Fornasari, Maria S
- Gibson, Toby J
- Gomes, Gregory-Neal W
- Gradinaru, Claudiu C
- Head-Gordon, Teresa
- Jensen, Malene Ringkjøbing
- Lemke, Edward A
- Longhi, Sonia
- Marino-Buslje, Cristina
- Minervini, Giovanni
- Mittag, Tanja
- Monzon, Alexander Miguel
- Pappu, Rohit V
- Parisi, Gustavo
- Ricard-Blum, Sylvie
- Ruff, Kiersten M
- Salladini, Edoardo
- Skepö, Marie
- Svergun, Dmitri
- Vallet, Sylvain D
- Varadi, Mihaly
- Tompa, Peter
- Tosatto, Silvio C E
- Piovesan, Damiano
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-12-10
- Volume
- 49
- Issue
- D1
- Pages
- D404-D411
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7778965
- OpenAlex
- W3112873140
- Cited by
- 142
- References
- 65
- Citations by year
- 2026: 12 · 2025: 18 · 2024: 20 · 2023: 35 · 2022: 34 · 2021: 20 · 2020: 3
- FWCI
- 7.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HAL AMU (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- HAL (submittedVersion)
- HAL (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion, cc-by-nc)
- Conicet (submittedVersion, cc-by-nc)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by-nc)
- Funders
- Italian Ministry of University and Research (2017483NH8)
- Horizon 2020 (778247, 871037)
- Hungarian Scientific Research Fund (K124670, K131702)
- Universidad Nacional de Quilmes (PUNQ 1309/19)
- National Agency for the Promotion of Science and Technology (PICT-2014-3430)
- LBC (PICT-2017-1924)
- Fondation pour la Recherche Médicale (DBI20141231336)
- Natural Sciences and Engineering Research Council of Canada (RGPIN 2017-0603)
- Agence Nationale de la Recherche (ANR-10-LABX-12-01)
- National Institutes of Health (5R01GM127627-03)
- German Ministry of Science and Education (16QK10A)
- Vrije Universiteit Brussel (SRP51)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- intrinsically disordered proteins, structural ensembles, database redesign, biocuration, metadata, search engines, DisProt
- MeSH terms
- Humans, Tumor Suppressor Protein p53, Databases, Protein, Search Engine, Intrinsically Disordered Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
