Features and development of Coot

Coot : model-building tools for molecular graphics

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A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos

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Structure deformation and curvature sensing of PIEZO1 in lipid membranes

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Structure, lipid scrambling activity and role in autophagosome formation of ATG9A

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Structural insights into HDAC6 tubulin deacetylation and its selective inhibition

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Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases

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Development of human cGAS-specific small-molecule inhibitors for repression of dsDNA-triggered interferon expression

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SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition

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Allosteric inhibition of SHP2: identification of a potent, selective, and orally efficacious phosphatase inhibitor

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Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors

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Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

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A wheat resistosome defines common principles of immune receptor channels

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High thermodynamic stability of parametrically designed helical bundles

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Active Pin1 is a key target of all-trans retinoic acid in acute promyelocytic leukemia and breast cancer

Wei, S., Kozono, S., Kats, L., Nechama, M., Li, W., Guarnerio, J., Luo, M., You, M.-H., Yao, Y., Kondo, A., et al. (2015) · Nature Medicine · doi:10.1038/nm.3839 · Cited by 272

NEDD8 nucleates a multivalent cullin–RING–UBE2D ubiquitin ligation assembly

Baek, K., Krist, D. T., Prabu, J. R., Hill, S., Klügel, M., Neumaier, L.-M., von Gronau, S., Kleiger, G., & Schulman, B. A. (2020) · Nature · doi:10.1038/s41586-020-2000-y · Cited by 270

Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA

Hashimoto, H., Wang, D., Horton, J. R., Zhang, X., Corces, V. G., & Cheng, X. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.004 · Cited by 268

Small-molecule-induced polymerization triggers degradation of BCL6

Słabicki, M., Yoon, H., Koeppel, J., Nitsch, L., Roy Burman, S. S., Di Genua, C., Donovan, K. A., Sperling, A. S., Hunkeler, M., Tsai, J. M., et al. (2020) · Nature · doi:10.1038/s41586-020-2925-1 · Cited by 270

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

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Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

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A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology

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Chemical remodeling of a cellular chaperone to target the active state of mutant KRAS

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The molecular basis of tight nuclear tethering and inactivation of cGAS

Zhao, B., Xu, P., Rowlett, C. M., Jing, T., Shinde, O., Lei, Y., West, A. P., Liu, W. R., & Li, P. (2020) · Nature · doi:10.1038/s41586-020-2749-z · Cited by 261

Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C

Sackton, K. L., Dimova, N., Zeng, X., Tian, W., Zhang, M., Sackton, T. B., Meaders, J., Pfaff, K. L., Sigoillot, F., Yu, H., et al. (2014) · Nature · doi:10.1038/nature13660 · Cited by 257

Structural Basis for Cholesterol Transport-like Activity of the Hedgehog Receptor Patched

Zhang, Y., Bulkley, D. P., Xin, Y., Roberts, K. J., Asarnow, D. E., Sharma, A., Myers, B. R., Cho, W., Cheng, Y., & Beachy, P. A. (2018) · Cell · doi:10.1016/j.cell.2018.10.026 · Cited by 239

Structure of a Pancreatic ATP-Sensitive Potassium Channel

Li, N., Wu, J.-X., Ding, D., Cheng, J., Gao, N., & Chen, L. (2017) · Cell · doi:10.1016/j.cell.2016.12.028 · Cited by 252

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators

Song, G., Yang, D., Wang, Y., de Graaf, C., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., et al. (2017) · Nature · doi:10.1038/nature22378 · Cited by 241

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease

Akiyama, B. M., Laurence, H. M., Massey, A. R., Costantino, D. A., Xie, X., Yang, Y., Shi, P.-Y., Nix, J. C., Beckham, J. D., & Kieft, J. S. (2016) · Science · doi:10.1126/science.aah3963 · Cited by 245

Structural basis for the inhibition of cGAS by nucleosomes

Kujirai, T., Zierhut, C., Takizawa, Y., Kim, R., Negishi, L., Uruma, N., Hirai, S., Funabiki, H., & Kurumizaka, H. (2020) · Science · doi:10.1126/science.abd0237 · Cited by 243

The monoclonal antibody combination REGEN-COV protects against SARS-CoV-2 mutational escape in preclinical and human studies

Copin, R., Baum, A., Wloga, E., Pascal, K. E., Giordano, S., Fulton, B. O., Zhou, A., Negron, N., Lanza, K., Chan, N., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.002 · Cited by 212

Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species

Wang, R., Zhang, Q., Ge, J., Ren, W., Zhang, R., Lan, J., Ju, B., Su, B., Yu, F., Chen, P., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.06.003 · Cited by 240

Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation

Pemovska, T., Johnson, E., Kontro, M., Repasky, G. A., Chen, J., Wells, P., Cronin, C. N., McTigue, M., Kallioniemi, O., Porkka, K., et al. (2015) · Nature · doi:10.1038/nature14119 · Cited by 234

Treating cat allergy with monoclonal IgG antibodies that bind allergen and prevent IgE engagement

Orengo, J. M., Radin, A. R., Kamat, V., Badithe, A., Ben, L. H., Bennett, B. L., Zhong, S., Birchard, D., Limnander, A., Rafique, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03636-8 · Cited by 237

Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay

Kim, M., Sandford, E., Gatica, D., Qiu, Y., Liu, X., Zheng, Y., Schulman, B. A., Xu, J., Semple, I., Ro, S.-H., et al. (2016) · eLife · doi:10.7554/elife.12245 · Cited by 225

Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer

Hobbs, G. A., Baker, N. M., Miermont, A. M., Thurman, R. D., Pierobon, M., Tran, T. H., Anderson, A. O., Waters, A. M., Diehl, J. N., Papke, B., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-1006 · Cited by 231

Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signalling

Lee, S., Choi, J., Mohanty, J., Sousa, L. P., Tome, F., Pardon, E., Steyaert, J., Lemmon, M. A., Lax, I., & Schlessinger, J. (2018) · Nature · doi:10.1038/nature25010 · Cited by 236

Discovery and characterization of highly potent and selective allosteric USP7 inhibitors

Gavory, G., O'Dowd, C. R., Helm, M. D., Flasz, J., Arkoudis, E., Dossang, A., Hughes, C., Cassidy, E., McClelland, K., Odrzywol, E., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2528 · Cited by 224

Structure-Based Discovery of SD-36 as a Potent, Selective, and Efficacious PROTAC Degrader of STAT3 Protein

Zhou, H., Bai, L., Xu, R., Zhao, Y., Chen, J., McEachern, D., Chinnaswamy, K., Wen, B., Dai, L., Kumar, P., et al. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b01530 · Cited by 233

Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer

LaMarche, M. J., Acker, M., Argintaru, A., Bauer, D., Boisclair, J., Chan, H., Chen, C. H.-T., Chen, Y.-N., Chen, Z., Deng, Z., et al. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01170 · Cited by 231

Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers

Papillon, J. P. N., Nakajima, K., Adair, C. D., Hempel, J., Jouk, A. O., Karki, R. G., Mathieu, S., Möbitz, H., Ntaganda, R., Smith, T., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01318 · Cited by 244

Cryo-EM structures of a human ABCG2 mutant trapped in ATP-bound and substrate-bound states

Manolaridis, I., Jackson, S. M., Taylor, N. M. I., Kowal, J., Stahlberg, H., & Locher, K. P. (2018) · Nature · doi:10.1038/s41586-018-0680-3 · Cited by 228

Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells

Ooi, J. D., Petersen, J., Tan, Y. H., Huynh, M., Willett, Z. J., Ramarathinam, S. H., Eggenhuizen, P. J., Loh, K. L., Watson, K. A., Gan, P. Y., et al. (2017) · Nature · doi:10.1038/nature22329 · Cited by 218

Structural basis for regulation of human acetyl-CoA carboxylase

Hunkeler, M., Hagmann, A., Stuttfeld, E., Chami, M., Guri, Y., Stahlberg, H., & Maier, T. (2018) · Nature · doi:10.1038/s41586-018-0201-4 · Cited by 229

Structural basis for GLP-1 receptor activation by LY3502970, an orally active nonpeptide agonist

Kawai, T., Sun, B., Yoshino, H., Feng, D., Suzuki, Y., Fukazawa, M., Nagao, S., Wainscott, D. B., Showalter, A. D., Droz, B. A., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2014879117 · Cited by 231

Structural mechanism of ergosterol regulation by fungal sterol transcription factor Upc2

Yang, H., Tong, J., Lee, C. W., Ha, S., Eom, S. H., & Im, Y. J. (2015) · Nature Communications · doi:10.1038/ncomms7129 · Cited by 223

Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction

Simonetta, K. R., Taygerly, J., Boyle, K., Basham, S. E., Padovani, C., Lou, Y., Cummins, T. J., Yung, S. L., von Soly, S. K., Kayser, F., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09358-9 · Cited by 217

Structural basis for the recognition of Sonic Hedgehog by human Patched1

Gong, X., Qian, H., Cao, P., Zhao, X., Zhou, Q., Lei, J., & Yan, N. (2018) · Science · doi:10.1126/science.aas8935 · Cited by 216

Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome

Passos, D. O., Li, M., Yang, R., Rebensburg, S. V., Ghirlando, R., Jeon, Y., Shkriabai, N., Kvaratskhelia, M., Craigie, R., & Lyumkis, D. (2017) · Science · doi:10.1126/science.aah5163 · Cited by 202

Structural basis for high-affinity binding of LEDGF PWWP to mononucleosomes

Eidahl, J. O., Crowe, B. L., North, J. A., McKee, C. J., Shkriabai, N., Feng, L., Plumb, M., Graham, R. L., Gorelick, R. J., Hess, S., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt074 · Cited by 207

Transferrin receptor 1 is a reticulocyte-specific receptor for Plasmodium vivax

Gruszczyk, J., Kanjee, U., Chan, L.-J., Menant, S., Malleret, B., Lim, N. T. Y., Schmidt, C. Q., Mok, Y.-F., Lin, K.-M., Pearson, R. D., et al. (2018) · Science · doi:10.1126/science.aan1078 · Cited by 212

Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14α-Demethylase

Sagatova, A. A., Keniya, M. V., Wilson, R. K., Monk, B. C., & Tyndall, J. D. A. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00925-15 · Cited by 210

Structures of the σ2 receptor enable docking for bioactive ligand discovery

Alon, A., Lyu, J., Braz, J. M., Tummino, T. A., Craik, V., O’Meara, M. J., Webb, C. M., Radchenko, D. S., Moroz, Y. S., Huang, X.-P., et al. (2021) · Nature · doi:10.1038/s41586-021-04175-x · Cited by 211

Structural basis for Cas9 off-target activity

Pacesa, M., Lin, C.-H., Cléry, A., Saha, A., Arantes, P. R., Bargsten, K., Irby, M. J., Allain, F. H.-T., Palermo, G., Cameron, P., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.026 · Cited by 198

De novo protein design enables the precise induction of RSV-neutralizing antibodies

Sesterhenn, F., Yang, C., Bonet, J., Cramer, J. T., Wen, X., Wang, Y., Chiang, C.-I., Abriata, L. A., Kucharska, I., Castoro, G., et al. (2020) · Science · doi:10.1126/science.aay5051 · Cited by 191

Lats1/2 Sustain Intestinal Stem Cells and Wnt Activation through TEAD-Dependent and Independent Transcription

Li, Q., Sun, Y., Jarugumilli, G. K., Liu, S., Dang, K., Cotton, J. L., Xiol, J., Chan, P. Y., DeRan, M., Ma, L., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.03.002 · Cited by 180

The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex

Halbach, F., Reichelt, P., Rode, M., & Conti, E. (2013) · Cell · doi:10.1016/j.cell.2013.07.017 · Cited by 210

Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule

Tsai, J. C., Miller-Vedam, L. E., Anand, A. A., Jaishankar, P., Nguyen, H. C., Renslo, A. R., Frost, A., & Walter, P. (2018) · Science · doi:10.1126/science.aaq0939 · Cited by 192

CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses

Lineburg, K. E., Grant, E. J., Swaminathan, S., Chatzileontiadou, D. S. M., Szeto, C., Sloane, H., Panikkar, A., Raju, J., Crooks, P., Rehan, S., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.04.006 · Cited by 183

Structural and mechanistic insights into fungal β-1,3-glucan synthase FKS1

Hu, X., Yang, P., Chai, C., Liu, J., Sun, H., Wu, Y., Zhang, M., Zhang, M., Liu, X., & Yu, H. (2023) · Nature · doi:10.1038/s41586-023-05856-5 · Cited by 213

Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular basis of antimalarial drug action

Birth, D., Kao, W.-C., & Hunte, C. (2014) · Nature Communications · doi:10.1038/ncomms5029 · Cited by 205

Tissue-Specific Oncogenic Activity of KRASA146T

Poulin, E. J., Bera, A. K., Lu, J., Lin, Y.-J., Strasser, S. D., Paulo, J. A., Huang, T. Q., Morales, C., Yan, W., Cook, J., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-18-1220 · Cited by 197

Structural Characterisation Reveals Mechanism of IL-13-Neutralising Monoclonal Antibody Tralokinumab as Inhibition of Binding to IL-13Rα1 and IL-13Rα2

Popovic, B., Breed, J., Rees, D. G., Gardener, M. J., Vinall, L. M. K., Kemp, B., Spooner, J., Keen, J., Minter, R., Uddin, F., et al. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.12.005 · Cited by 198

Histone deacetylase 10 structure and molecular function as a polyamine deacetylase

Hai, Y., Shinsky, S. A., Porter, N. J., & Christianson, D. W. (2017) · Nature Communications · doi:10.1038/ncomms15368 · Cited by 200

Structure of a RING E3 Trapped in Action Reveals Ligation Mechanism for the Ubiquitin-like Protein NEDD8

Scott, D. C., Sviderskiy, V. O., Monda, J. K., Lydeard, J. R., Cho, S. E., Harper, J. W., & Schulman, B. A. (2014) · Cell · doi:10.1016/j.cell.2014.04.037 · Cited by 201

ABCG2 transports anticancer drugs via a closed-to-open switch

Orlando, B. J., & Liao, M. (2020) · Nature Communications · doi:10.1038/s41467-020-16155-2 · Cited by 198

Structure-guided development of a potent and selective non-covalent active-site inhibitor of USP7.

Lamberto, I., Liu, X., Seo, H.-S., Schauer, N. J., Iacob, R. E., Hu, W., Das, D., Mikhailova, T., Weisberg, E. L., Engen, J. R., et al. (2017) · Cell Chemical Biology · doi:10.1016/j.chembiol.2017.09.003 · Cited by 192

Structures of human Patched and its complex with native palmitoylated sonic hedgehog

Qi, X., Schmiege, P., Coutavas, E., Wang, J., & Li, X. (2018) · Nature · doi:10.1038/s41586-018-0308-7 · Cited by 178

Specificity of Linear Motifs That Bind to a Common Mitogen-Activated Protein Kinase Docking Groove

Garai, Á., Zeke, A., Gógl, G., Törő, I., Fördős, F., Blankenburg, H., Bárkai, T., Varga, J., Alexa, A., Emig, D., et al. (2012) · Science Signaling · doi:10.1126/scisignal.2003004 · Cited by 177

Selective PP2A enhancement through biased heterotrimer stabilization

Leonard, D., Huang, W., Izadmehr, S., O’Connor, C. M., Wiredja, D. D., Wang, Z., Zaware, N., Chen, Y., Schlatzer, D. M., Kiselar, J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.03.038 · Cited by 176

Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

Laverty, D., Thomas, P., Field, M., Andersen, O. J., Gold, M. G., Biggin, P. C., Gielen, M., & Smart, T. G. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3477 · Cited by 179

Ubiquitin ligation to F-box protein targets by SCF–RBR E3–E3 super-assembly

Horn-Ghetko, D., Krist, D. T., Prabu, J. R., Baek, K., Mulder, M. P. C., Klügel, M., Scott, D. C., Ovaa, H., Kleiger, G., & Schulman, B. A. (2021) · Nature · doi:10.1038/s41586-021-03197-9 · Cited by 187

Structural basis of splicing modulation by antitumor macrolide compounds

Cretu, C., Agrawal, A. A., Cook, A., Will, C. L., Fekkes, P., Smith, P. G., Lührmann, R., Larsen, N., Buonamici, S., & Pena, V. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.011 · Cited by 174

Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut

Foley, M. H., Walker, M. E., Stewart, A. K., O’Flaherty, S., Gentry, E. C., Patel, S., Beaty, V. V., Allen, G., Pan, M., Simpson, J. B., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01337-7 · Cited by 181

Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins

Gault, J., Liko, I., Landreh, M., Shutin, D., Bolla, J. R., Jefferies, D., Agasid, M., Yen, H.-Y., Ladds, M. J. G. W., Lane, D. P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0821-0 · Cited by 171

Structural basis for IL-12 and IL-23 receptor sharing reveals a gateway for shaping actions on T versus NK cells

Glassman, C. R., Mathiharan, Y. K., Jude, K. M., Su, L., Panova, O., Lupardus, P. J., Spangler, J. B., Ely, L. K., Thomas, C., Skiniotis, G., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.018 · Cited by 181

Indole-3-acetaldehyde dehydrogenase-dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000

McClerklin, S. A., Lee, S. G., Harper, C. P., Nwumeh, R., Jez, J. M., & Kunkel, B. N. (2018) · PLOS Pathogens · doi:10.1371/journal.ppat.1006811 · Cited by 182

Protein sequence design with a learned potential

Anand, N., Eguchi, R., Mathews, I. I., Perez, C. P., Derry, A., Altman, R. B., & Huang, P.-S. (2022) · Nature Communications · doi:10.1038/s41467-022-28313-9 · Cited by 171

Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

Tailford, L. E., Owen, C. D., Walshaw, J., Crost, E. H., Hardy-Goddard, J., Le Gall, G., de Vos, W. M., Taylor, G. L., & Juge, N. (2015) · Nature Communications · doi:10.1038/ncomms8624 · Cited by 183

Targeting cancer with small-molecule pan-KRAS degraders

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Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils

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