IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

Extreme disorder in an ultrahigh-affinity protein complex

Borgia, A., Borgia, M. B., Bugge, K., Kissling, V. M., Heidarsson, P. O., Fernandes, C. B., Sottini, A., Soranno, A., Buholzer, K. J., Nettels, D., et al. (2018) · Nature · doi:10.1038/nature25762 · Cited by 653

Oxidation of the zinc-thiolate complex and uncoupling of endothelial nitric oxide synthase by peroxynitrite

Zou, M.-H., Shi, C., & Cohen, R. A. (2002) · Journal of Clinical Investigation · doi:10.1172/jci0214442 · Cited by 494

FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies

Miskei, M., Antal, C., & Fuxreiter, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1019 · Cited by 119

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · doi:10.1101/2021.06.14.448402 · Cited by 5,549

α‐Synuclein aggregation nucleates through liquid‐liquid phase separation

Ray, S., Singh, N., Kumar, R., Patel, K., Pandey, S., Datta, D., Mahato, J., Panigrahi, R., Navalkar, A., Mehra, S., et al. (2020) · Nature Chemistry · doi:10.1038/s41557-020-0465-9 · Cited by 863

A structural biology community assessment of AlphaFold2 applications

Akdel, M., Pires, D. E. V., Pardo, E. P., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00849-w · Cited by 675

OpenCell: Endogenous tagging for the cartography of human cellular organization

Cho, N. H., Cheveralls, K. C., Brunner, A.-D., Kim, K., Michaelis, A. C., Raghavan, P., Kobayashi, H., Savy, L., Li, J. Y., Canaj, H., et al. (2022) · Science · doi:10.1126/science.abi6983 · Cited by 567

Phase separation and neurodegenerative diseases: a disturbance in the force

Zbinden, A., Pérez-Berlanga, M., De Rossi, P., & Polymenidou, M. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.09.014 · Cited by 500

Critical assessment of protein intrinsic disorder prediction

Necci, M., Piovesan, D., Predictors, C., Hoque, M. T., Walsh, I., Iqbal, S., Vendruscolo, M., Sormanni, P., Wang, C., Raimondi, D., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01117-3 · Cited by 343

Nascent Pre-rRNA sorting via phase separation drives the assembly of dense fibrillar components in the human nucleolus

Yao, R.-W., Xu, G., Wang, Y., Shan, L., Luan, P.-F., Wang, Y., Wu, M., Yang, L.-Z., Xing, Y.-H., Yang, L., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.08.014 · Cited by 327

In-cell architecture of an actively transcribing-translating expressome

O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284

AlphaFold2 models indicate that protein sequence determines both structure and dynamics

Guo, H.-B., Perminov, A., Bekele, S., Kedziora, G., Farajollahi, S., Varaljay, V., Hinkle, K., Molinero, V., Meister, K., Hung, C., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-14382-9 · Cited by 248

Systematic 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

Intrinsically disordered proteins play diverse roles in cell signaling

Bondos, S. E., Dunker, A. K., & Uversky, V. N. (2022) · Cell Communication and Signaling · doi:10.1186/s12964-022-00821-7 · Cited by 222

Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses

(2023) · doi:10.1038/s41564-022-01287-6 · Cited by 215

Tau liquid‐liquid phase separation in neurodegenerative diseases

Boyko, S., & Surewicz, W. K. (2022) · Trends in Cell Biology · doi:10.1016/j.tcb.2022.01.011 · Cited by 215

Visualizing translation dynamics at atomic detail inside a bacterial cell

Xue, L., Lenz, S., Zimmermann-Kogadeeva, M., Tegunov, D., Cramer, P., Bork, P., Rappsilber, J., & Mahamid, J. (2022) · Nature · doi:10.1038/s41586-022-05255-2 · Cited by 184

Twenty Years of SynGAP Research: From Synapses to Cognition

Gamache, T. R., Araki, Y., & Huganir, R. L. (2020) · The Journal of Neuroscience · doi:10.1523/jneurosci.0420-19.2020 · Cited by 161

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

Hanson, J., Paliwal, K. K., Litfin, T., & Zhou, Y. (2019) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.01.004 · Cited by 165

Improving peptide-protein docking with AlphaFold-Multimer using forced sampling

Johansson-Åkhe, I., & Wallner, B. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.959160 · Cited by 162

Intrinsic protein disorder and conditional folding in AlphaFoldDB

Piovesan, D., Monzon, A. M., & Tosatto, S. C. E. (2022) · Protein Science · doi:10.1002/pro.4466 · Cited by 160

A structural biology community assessment of AlphaFold 2 applications

Akdel, M., Pires, D. E. V., Porta Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., et al. (2021) · doi:10.1101/2021.09.26.461876 · Cited by 122

The structural coverage of the human proteome before and after AlphaFold

Porta-Pardo, E., Ruiz-Serra, V., Valentini, S., & Valencia, A. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009818 · Cited by 131

Conformational buffering underlies functional selection in intrinsically disordered protein regions

González-Foutel, N. S., Glavina, J., Borcherds, W. M., Safranchik, M., Barrera-Vilarmau, S., Sagar, A., Estaña, A., Barozet, A., Garrone, N. A., Fernandez-Ballester, G., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00811-w · Cited by 118

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome

Lau, E., Han, Y., Williams, D. R., Thomas, C. T., Shrestha, R., Wu, J. C., & Lam, M. P. Y. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.026 · Cited by 67

Mitochondria-dependent phase separation of disease-relevant proteins drives pathological features of age-related macular degeneration

La Cunza, N., Tan, L. X., Thamban, T., Germer, C. J., Rathnasamy, G., Toops, K. A., & Lakkaraju, A. (2021) · JCI Insight · doi:10.1172/jci.insight.142254 · Cited by 65

A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates

Rebak, A. S., Hendriks, I. A., Elsborg, J. D., Buch-Larsen, S. C., Nielsen, C. H., Terslev, L., Kirsch, R., Damgaard, D., Doncheva, N. T., Lennartsson, C., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01214-9 · Cited by 45

Regulatory sites in the Mon1–Ccz1 complex control Rab5 to Rab7 transition and endosome maturation

Borchers, A.-C., Janz, M., Schäfer, J.-H., Moeller, A., Kümmel, D., Paululat, A., Ungermann, C., & Langemeyer, L. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2303750120 · Cited by 43

Phase separation and ageing of glycine-rich protein from tick adhesive

Ganar, K. A., Nandy, M., Turbina, P., Chen, C., Suylen, D., Nihoul, E., Pascoe, E. L., van der Beelen, S., Plaum, M., van den Bos, L., et al. (2025) · Nature Chemistry · doi:10.1038/s41557-024-01686-8 · Cited by 42

Identifying common transcriptome signatures of cancer by interpreting deep learning models

Jha, A., Quesnel-Vallières, M., Wang, D., Thomas-Tikhonenko, A., Lynch, K. W., & Barash, Y. (2022) · Genome Biology · doi:10.1186/s13059-022-02681-3 · Cited by 39

A promiscuous mechanism to phase separate eukaryotic carbon fixation in the green lineage

Barrett, J., Naduthodi, M. I. S., Mao, Y., Dégut, C., Musiał, S., Salter, A., Leake, M. C., Plevin, M. J., McCormick, A. J., Blaza, J. N., et al. (2024) · Nature Plants · doi:10.1038/s41477-024-01812-x · Cited by 37

A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation

Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42049-0 · Cited by 33

Cyclophilin A supports translation of intrinsically disordered proteins and affects haematopoietic stem cell ageing

Maneix, L., Iakova, P., Lee, C. G., Moree, S. E., Lu, X., Datar, G. K., Hill, C. T., Spooner, E., King, J. C. K., Sykes, D. B., et al. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01387-x · Cited by 28

Protein embeddings predict binding residues in disordered regions

(2024) · doi:10.1038/s41598-024-64211-4 · Cited by 27

Orchestrated actin nucleation by the Candida albicans polarisome complex enables filamentous growth

Xie, Y., Loh, Z. Y., Xue, J., Zhou, F., Sun, J., Qiao, Z., Jin, S., Deng, Y., Li, H., Wang, Y., et al. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.013890 · Cited by 26

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac187 · Cited by 25

The Chromatin Regulator HMGA1a Undergoes Phase Separation in the Nucleus**

Zhu, H., Narita, M., Joseph, J. A., Krainer, G., Arter, W. E., Olan, I., Saar, K. L., Ermann, N., Espinosa, J. R., Shen, Y., et al. (2023) · ChemBioChem · doi:10.1002/cbic.202200450 · Cited by 23

Global Population Genomics of Two Subspecies of Cryptosporidium hominis during 500 Years of Evolution

Tichkule, S., Cacciò, S. M., Robinson, G., Chalmers, R. M., Mueller, I., Emery-Corbin, S. J., Eibach, D., Tyler, K. M., van Oosterhout, C., & Jex, A. R. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac056 · Cited by 23

Large-Scale Discovery of Microbial Fibrillar Adhesins and Identification of Novel Members of Adhesive Domain Families

(2022) · doi:10.1128/jb.00107-22 · Cited by 23

Heterologous expression of naturally evolved putative de novo proteins with chaperones

Eicholt, L. A., Aubel, M., Berk, K., Bornberg‐Bauer, E., & Lange, A. (2022) · Protein Science · doi:10.1002/pro.4371 · Cited by 18

Intrinsic Disorder as a Natural Preservative: High Levels of Intrinsic Disorder in Proteins Found in the 2600-Year-Old Human Brain

(2022) · doi:10.3390/biology11121704 · Cited by 17

Orchestration of algal metabolism by protein disorder

Launay, H., Receveur-Bréchot, V., Carrière, F., & Gontero, B. (2019) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2019.108070 · Cited by 16

Hidden information on protein function in censuses of proteome foldedness

Cox, D., Ang, C.-S., Nillegoda, N. B., Reid, G. E., & Hatters, D. M. (2022) · Nature Communications · doi:10.1038/s41467-022-29661-2 · Cited by 16

Chaotic aging: intrinsically disordered proteins in aging-related processes

Manyilov, V. D., Ilyinsky, N. S., Nesterov, S. V., Saqr, B. M. G. A., Dayhoff, G. W., Zinovev, E. V., Matrenok, S. S., Fonin, A. V., Kuznetsova, I. M., Turoverov, K. K., et al. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04897-3 · Cited by 14

AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein

Guo, H.-B., Huntington, B., Perminov, A., Smith, K., Hastings, N., Dennis, P., Kelley-Loughnane, N., & Berry, R. (2024) · PLOS ONE · doi:10.1371/journal.pone.0301866 · Cited by 13

Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock

Tariq, D., Maurici, N., Bartholomai, B. M., Chandrasekaran, S., Dunlap, J. C., Bah, A., & Crane, B. R. (2024) · eLife · doi:10.7554/elife.90259 · Cited by 13

Comprehensive Analysis of the Structure and Function of Peptide:N-Glycanase 1 and Relationship with Congenital Disorder of Deglycosylation

Miao, X., Wu, J., Chen, H., & Lu, G. (2022) · Nutrients · doi:10.3390/nu14091690 · Cited by 13

Investigating the conformational dynamics of Zika virus NS4B protein

(2022) · doi:10.1016/j.virol.2022.08.005 · Cited by 13

DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features

Luppino, F., Adzhubei, I. A., Cassa, C. A., & Toth-Petroczy, A. (2023) · Nature Communications · doi:10.1038/s41467-023-37661-z · Cited by 12

Pathological mutations reveal the key role of the cytosolic iRhom2 N-terminus for phosphorylation-independent 14-3-3 interaction and ADAM17 binding, stability, and activity

Bläsius, K., Ludwig, L., Knapp, S., Flaßhove, C., Sonnabend, F., Keller, D., Tacken, N., Gao, X., Kahveci-Türköz, S., Grannemann, C., et al. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05132-3 · Cited by 12

Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties

Li, X.-H., Yu, C. W. H., Gomez-Navarro, N., Stancheva, V., Zhu, H., Murthy, A., Wozny, M., Malhotra, K., Johnson, C. M., Blackledge, M., et al. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgae006 · Cited by 11

Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping

Foran, G., Hallam, R. D., Megaly, M., Turgambayeva, A., Antfolk, D., Li, Y., Luca, V. C., & Necakov, A. (2024) · Scientific Reports · doi:10.1038/s41598-024-71634-6 · Cited by 11

The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs

(2024) · doi:10.1021/acs.biochem.3c00510 · Cited by 9

SLiMAn: An Integrative Web Server for Exploring Short Linear Motif-Mediated Interactions in Interactomes

Reys, V., & Labesse, G. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00964 · Cited by 9

Structural and functional analysis of the human cone‐rod homeobox transcription factor

(2022) · doi:10.1002/prot.26332 · Cited by 9

Plasmodium sporozoites require the protein B9 to invade hepatocytes

(2023) · doi:10.1016/j.isci.2023.106056 · Cited by 8

RLIP76: A Structural and Functional Triumvirate

Cornish, J., Owen, D., & Mott, H. R. (2021) · Cancers · doi:10.3390/cancers13092206 · Cited by 8

Recurrent evolution of selfishness from an essential tRNA synthetase in Caenorhabditis tropicalis

Tikanova, P., Ross, J. J., Hagmüller, A., Pühringer, F., Pliota, P., Krogull, D., Stefania, V., Hunold, M., Koreshova, A., Koller, A., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02894-2 · Cited by 7

Molecular determinants of TRAF6 binding specificity suggest that native interaction partners are not optimized for affinity

Halpin, J. C., Whitney, D., Rigoldi, F., Sivaraman, V., Singer, A., & Keating, A. E. (2022) · Protein Science · doi:10.1002/pro.4429 · Cited by 7

Mutational scan inferred binding energetics and structure in intrinsically disordered protein CcdA

Chandra, S., Manjunath, K., Asok, A., & Varadarajan, R. (2023) · Protein Science · doi:10.1002/pro.4580 · Cited by 7

AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants

Ali, M. A., & Caetano-Anollés, G. (2024) · Viruses · doi:10.3390/v16091358 · Cited by 6

Elaboration of the Homer1 recognition landscape reveals incomplete divergence of paralogous EVH1 domains

Singer, A., Ramos, A., & Keating, A. E. (2024) · Protein Science · doi:10.1002/pro.5094 · Cited by 6

Looking at the Pathogenesis of the Rabies Lyssavirus Strain Pasteur Vaccins through a Prism of the Disorder-Based Bioinformatics

Dhulipala, S., & Uversky, V. N. (2022) · Biomolecules · doi:10.3390/biom12101436 · Cited by 6

I-Shaped Dimers of a Plant Chloroplast FOF1-ATP Synthase in Response to Changes in Ionic Strength

Osipov, S. D., Ryzhykau, Y. L., Zinovev, E. V., Minaeva, A. V., Ivashchenko, S. D., Verteletskiy, D. P., Sudarev, V. V., Kuklina, D. D., Nikolaev, M. Y., Semenov, Y. S., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241310720 · Cited by 5

AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits

(2025) · doi:10.1126/sciadv.adx0796 · Cited by 4

Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into their in-vivo functions

Ruiz-Molina, N., Parsons, J., Decker, E. L., & Reski, R. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.002 · Cited by 4

RG motifs promote piRNA-mediated gene silencing in C. elegans

Wallis, D. C., & Phillips, C. M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1331 · Cited by 3

Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships

Sabsay, K. R., & te Velthuis, A. J. W. (2024) · Virus Evolution · doi:10.1093/ve/veae058 · Cited by 3

Molecular genomic insights into melanoma associated proteins PRAME and BAP1

Nawn, D., Hassan, S. S., Hromić-Jahjefendić, A., Bhattacharya, T., Basu, P., Redwan, E. M., Barh, D., Andrade, B. S., Aljabali, A. A., Serrano-Aroca, Á., et al. (2025) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2025.2475228 · Cited by 3

Protein structure and selection pressure in plants: using mutation to understand the functional importance of protein structure

Long, E., & Monroe, G. (2026) · BMC Genomics · doi:10.1186/s12864-026-12674-2 · Cited by 3

Coronaviruses spike glycoprotein endodomains: The sequence and structure‐based comprehensive study

Kumar, P., Bhardwaj, A., Mukherjee, B., Joshi, R., & Giri, R. (2023) · Protein Science · doi:10.1002/pro.4804 · Cited by 2

Structural analysis of genomic and proteomic signatures reveal dynamic expression of intrinsically disordered regions in breast cancer

Zatorski, N., Sun, Y., Elmas, A., Dallago, C., Karl, T., Stein, D., Rost, B., Huang, K.-L., Walsh, M., & Schlessinger, A. (2024) · iScience · doi:10.1016/j.isci.2024.110640 · Cited by 2

Pathogenic variations illuminate functional constraints in intrinsically disordered proteins

(2026) · doi:10.1016/j.isci.2026.115215 · Cited by 2

Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock

(2022) · doi:10.1101/2022.11.03.515097 · Cited by 1

The N-terminal region of malaria vaccine candidate asparagine-rich merozoite antigen is immunodominant and targeted by polyreactive antibodies

Garza, R., Marchioni, J. M., Honeycutt, J. D., Hurlburt, N. K., Torres, C., Garcia, A., Neog, S., Loranc, E., Yemington, E., Towers, D., et al. (2026) · Disease Models & Mechanisms · doi:10.1242/dmm.052979 · Cited by 1

An integrative multitiered computational analysis for better understanding the structure and function of 85 miniproteins

Veluri, R., Pollin, G., Wagenknecht, J. B., Urrutia, R., & Zimmermann, M. T. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf178 · Cited by 1

Protein tandem repeats that produce frameshifts can generate new structural states and functions

Osmanli, Z., Aldrian, G., Leclercq, J., Falgarone, T., Gómez Bergna, S. M., Prada Gori, D. N., Oleinikov, A. V., Shahmuradov, I., & Kajava, A. V. (2026) · The FEBS Journal · doi:10.1111/febs.70273