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UCSF ChimeraX Citations

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Selected Citations

Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes. Zhu X, Cruz VE et al. Science. 2024 Nov 22;386(6724):eadq8587.

Structure of the human TIP60-C histone exchange and acetyltransferase complex. Li C, Smirnova E et al. Nature. 2024 Nov 21;635(8039):764-769.

Quantifying constraint in the human mitochondrial genome. Lake NJ, Ma K et al. Nature. 2024 Nov 14;635(8038):390-397.

Engineered odorant receptors illuminate the basis of odour discrimination. de March CA, Ma N et al. Nature. 2024 Nov 14;635(8038):499–508.

Diverse anti-defence systems are encoded in the leading region of plasmids. Samuel B, Mittelman K et al. Nature. 2024 Nov 7;635(8037):186-192.

Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome. Rogalska ME, Mancini E et al. Science. 2024 Nov 1;386(6721):551-560.

The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Wang F, He Q et al. Struct Mol Biol. 2024 Nov;31(11):1680-1691

LYCHOS is a human hybrid of a plant-like PIN transporter and a GPCR. Bayly-Jones C, Lupton CJ et al. Nature. 2024 Oct 31;634(8036):1238–1244.

Glucose-sensitive insulin with attenuation of hypoglycaemia. Hoeg-Jensen T, Kruse T et al. Nature. 2024 Oct 24;634(8035):944-951.

A brain-to-gut signal controls intestinal fat absorption. Lyu Q, Xue W et al. Nature. 2024 Oct 24;634(8035):936-943.

Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP type C. Arseni D, Nonaka T et al. Nature. 2024 Oct 17;634(8034):662–668.

Structure of a fully assembled γδ T cell antigen receptor. Gully BS, Ferreira Fernandes J et al. Nature. 2024 Oct 17;634(8034):729–736.

A virally encoded tRNA neutralizes the PARIS antiviral defence system. Burman N, Belukhina S et al. Nature. 2024 Oct 10;634(8033):424–431.

Architecture and activation mechanism of the bacterial PARIS defence system. Deep A, Liang Q et al. Nature. 2024 Oct 10;634(8033):432–439.

Intragenic DNA inversions expand bacterial coding capacity. Chanin RB, West PT et al. Nature. 2024 Oct 3;634(8032):234–242.

Structural insights into the human P2X1 receptor and ligand interactions. Bennetts FM, Venugopal H et al. Nat Commun. 2024 Sep 28;15(1):8418.

Mutating a flexible region of the RSV F protein can stabilize the prefusion conformation. Liang Y, Shao S et al. Science. 2024 Sep 27;385(6716):1484-1491.

Structural insights into the high-affinity IgE receptor FcεRI complex. Deng M, Du S et al. Nature. 2024 Sep 26;633(8031):952–959.

Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. Brouwer PJM, Perrett HR et al. Cell Rep. 2024 Sep 24;43(9):114708.

Large library docking identifies positive allosteric modulators of the calcium-sensing receptor. Liu F, Wu CG et al. Science. 2024 Sep 20;385(6715):eado1868.

Targeting cancer with small-molecule pan-KRAS degraders. Popow J, Farnaby W et al. Science. 2024 Sep 20;385(6715):1338-1347.

NAC guides a ribosomal multienzyme complex for nascent protein processing. Lentzsch AM, Yudin D et al. Nature. 2024 Sep 19;633(8030):718–724.

Mapping glycoprotein structure reveals Flaviviridae evolutionary history. Mifsud JCO, Lytras S et al. Nature. 2024 Sep 19;633(8030):695–703.

SymProFold: Structural prediction of symmetrical biological assemblies. Buhlheller C, Sagmeister T et al. Nat Commun. 2024 Sep 18;15(1):8152.

Inherent symmetry and flexibility in hepatitis B virus subviral particles. Wang Q, Wang T et al. Science. 2024 Sep 13;385(6714):1217-1224.

Substrate binding and inhibition mechanism of norepinephrine transporter. Ji W, Miao A et al. Nature. 2024 Sep 12;633(8029):473–479.

In situ structure and rotary states of mitochondrial ATP synthase in whole Polytomella cells. Dietrich L, Agip AA et al. Science. 2024 Sep 6;385(6713):1086-1090.

Structural basis for transthiolation intermediates in the ubiquitin pathway. Kochańczyk T, Hann ZS et al. Nature. 2024 Sep 5;633(8028):216–223.

Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site. Caniels TG, Medina-Ramìrez M et al. Sci Immunol. 2024 Aug 30;9(98):eadk9550.

Cultivation and visualization of a methanogen of the phylum Thermoproteota. Kohtz AJ, Petrosian N et al. Nature. 2024 Aug 29;632(8027):1118–1123.

Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Yang Z, Mameri A et al. Science. 2024 Aug 23;385(6711):eadl5816.

De novo design of allosterically switchable protein assemblies. Pillai A, Idris A et al. Nature. 2024 Aug 22;632(8026):911–920.

Molecular basis of human noradrenaline transporter reuptake and inhibition. Tan J, Xiao Y et al. Nature. 2024 Aug 22;632(8026):921–929.

Generative artificial intelligence performs rudimentary structural biology modeling. Ille AM, Markosian C et al. Sci Rep. 2024 Aug 21;14(1):19372.

Atomic structures of a bacteriocin targeting Gram-positive bacteria. Cai X, He Y et al. Nat Commun. 2024 Aug 16;15(1):7057.

Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Grunst MW, Qin Z et al. Science. 2024 Aug 16;385(6710):757-765.

Structure of the human dopamine transporter in complex with cocaine. Nielsen JC, Salomon K et al. Nature. 2024 Aug 15;632(8025):678-685.

Mechanism of allosteric inhibition of human p97/VCP ATPase and its disease mutant by triazole inhibitors. Nandi P, DeVore K et al. Commun Chem. 2024 Aug 9;7(1):177.

Propofol rescues voltage-dependent gating of HCN1 channel epilepsy mutants. Kim ED, Wu X et al. Nature. 2024 Aug 8;632(8024):451–459.

Mechanism for the initiation of spliceosome disassembly. Vorländer MK, Rothe P et al. Nature. 2024 Aug 8;632(8024):443–450.

Poc1 bridges basal body inner junctions to promote triplet microtubule integrity and connections. Ruehle MD, Li S et al. J Cell Biol. 2024 Aug 5;223(8):e202311104.

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases. Yoon PH, Zhang Z et al. Science. 2024 Aug 2;385(6708):538-543.

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX. Read RJ, Pettersen EF et al. Acta Crystallogr D Struct Biol. 2024 Aug 1;80(Pt 8):588-598.

High-resolution yeast actin structures indicate the molecular mechanism of actin filament stiffening by cations. Xu XP, Cao W et al. Commun Chem. 2024 Jul 30;7(1):164.

Structure and topography of the synaptic V-ATPase-synaptophysin complex. Wang C, Jiang W et al. Nature. 2024 Jul 25;631(8022):899–904.

CryoET of β-amyloid and tau within postmortem Alzheimer's disease brain. Gilbert MAG, Fatima N et al. Nature. 2024 Jul 25;631(8022):913–919.

Purification and cryo-electron microscopy analysis of bacterial appendages. Sanchez JC, Baumgardt JK, Wright ER. Bio Protoc. 2024 Jul 20;14(14):e5032.

Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. Lin Z, Schaefer K et al. Science. 2024 Jul 19;385(6706):eadl5763.

Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Birkholz N, Kamata K et al. Nature. 2024 Jul 18;631(8021):670-677.

Computational design of soluble and functional membrane protein analogues. Goverde CA, Pacesa M et al. Nature. 2024 Jul 11;631(8020):449–458.

Inhibition of M. tuberculosis and human ATP synthase by BDQ and TBAJ-587. Zhang Y, Lai Y et al. Nature. 2024 Jul 11;631(8020):409–414.

A metabolic dependency of EBV can be targeted to hinder B cell transformation. Müller-Durovic B, Jäger J et al. Science. 2024 Jul 5;385(6704):eadk4898.

An alternative broad-specificity pathway for glycan breakdown in bacteria. Nasseri SA, Lazarski AC et al. Nature. 2024 Jul 4;631(8019):199–206.

Molecular plasticity of herpesvirus nuclear egress analysed in situ. Pražák V, Mironova Y et al. Nat Microbiol. 2024 Jul;9(7):1842-1855.

A neutralizing antibody prevents postfusion transition of measles virus fusion protein. Zyla DS, Della Marca R et al. Science. 2024 Jun 28;384(6703):eadm8693.

Plasmid targeting and destruction by the DdmDE bacterial defence system. Bravo JPK, Ramos DA et al. Nature. 2024 Jun 27;630(8018):961–967.

Structural mechanism of bridge RNA-guided recombination. Hiraizumi M, Perry NT et al. Nature. 2024 Jun 27;630(8018):994-1002.

AlphaFold2 structures guide prospective ligand discovery. Lyu J, Kapolka N et al. Science. 2024 Jun 21;384(6702):eadn6354.

Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Hussein R, Graça A et al. Science. 2024 Jun 21;384(6702):1349-1355.

Structural analysis of the dynamic ribosome-translocon complex. Lewis AJO, Zhong F et al. eLife. 2024 Jun 18;13:RP95814.

Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Grba DN, Wright JJ et al. Science. 2024 Jun 14;384(6701):1247-1253.

Molecular mechanism of choline and ethanolamine transport in humans. Ri K, Weng TH et al. Nature. 2024 Jun 13;630(8016):501–508.

Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Zhang S, Sun A et al. Nature. 2024 Jun 13;630(8016):484–492.

Structures of human γδ T cell receptor-CD3 complex. Xin W, Huang B et al. Nature. 2024 Jun 6;629(8015):222–229.

Dimerization and antidepressant recognition at noradrenaline transporter. Zhang H, Yin YL et al. Nature. 2024 Jun 6;629(8015):247–254.

Membraneless channels sieve cations in ammonia-oxidizing marine archaea. von Kügelgen A, Cassidy CK et al. Nature. 2024 Jun 6;629(8015):230–236.

The intrinsic substrate specificity of the human tyrosine kinome. Yaron-Barir TM, Joughin BA et al. Nature. 2024 May 30;629(8014):1174–1181.

Time-resolved cryo-EM of G-protein activation by a GPCR. Papasergi-Scott MM, Pérez-Hernández G et al. Nature. 2024 May 30;629(8014):1182–1191.

Computationally restoring the potency of a clinical antibody against Omicron. Desautels TA, Arrildt KT et al. Nature. 2024 May 23;629(8013):878–885.

Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Liang CC, Greenhough LA et al. Nature. 2024 May 16;629(8012):697–703.

Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. Keown J, Baazaoui A et al. J Virol. 2024 May 14;98(5):e0013824.

Structures and activation mechanism of the Gabija anti-phage system. Li J, Cheng R et al. Nature. 2024 May 9;629(8011):467–473.

Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. Ketaren NE, Mast FD et al. eLife. 2024 May 7;12:RP89423.

Streptomyces umbrella toxin particles block hyphal growth of competing species. Zhao Q, Bertolli S et al. Nature. 2024 May 2;629(8010):165–173.

Structural basis of Integrator-dependent RNA polymerase II termination. Fianu I, Ochmann M et al. Nature. 2024 May 2;629(8010):219–227.

Mechanical activation opens a lipid-lined pore in OSCA ion channels. Han Y, Zhou Z et al. Nature. 2024 Apr 25;628(8009):910–918.

Molecular insights into capsular polysaccharide secretion. Kuklewicz J, Zimmer J. Nature. 2024 Apr 25;628(8009):901–909.

Bond analysis in meta- and para-substituted thiophenols: overlap descriptors, local mode analysis, and QTAIM. Barbosa WG, Santos-Jr CV et al. J Mol Model. 2024 Apr 19;30(5):139.

Structure and assembly of a bacterial gasdermin pore. Johnson AG, Mayer ML et al. Nature. 2024 Apr 18;628(8008):657–663.

Bitter taste receptor activation by cholesterol and an intracellular tastant. Kim Y, Gumpper RH et al. Nature. 2024 Apr 18;628(8008):664–671.

Molecular mechanism of actin filament elongation by formins. Oosterheert W, Boiero Sanders M et al. Science. 2024 Apr 12;384(6692):eadn9560.

Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Vayssières M, Marechal N et al. Science. 2024 Apr 12;384(6692):227-232.

Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. Radko-Juettner S, Yue H et al. Nature. 2024 Apr 11;628(8007):442–449.

Removal of Pseudomonas type IV pili by a small RNA virus. Thongchol J, Yu Z et al. Science. 2024 Apr 5;384(6691):eadl0635.

Cryo-EM structures of RAD51 assembled on nucleosomes containing a DSB site. Shioi T, Hatazawa S et al. Nature. 2024 Apr 4;628(8006):212–220.

Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Lauber F, Deme JC et al. Nat Microbiol. 2024 Apr;9(4):1089-1102.

Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. Calise SJ, O'Neill AG et al. J Cell Biol. 2024 Apr 1;223(4):e202310139.

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Xu P, Liu Y et al. Nature. 2024 Mar 28;627(8005):873–879.

Continuous evolution of compact protein degradation tags regulated by selective molecular glues. Mercer JAM, DeCarlo SJ et al. Science. 2024 Mar 15;383(6688):eadk4422.

Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Bai R, Yuan M et al. Science. 2024 Mar 15;383(6688):1245-1252.

UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. DaRosa PA, Penchev I et al. Nature. 2024 Mar 14;627(8003):445–452.

The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. Makhlouf L, Peter JJ et al. Nature. 2024 Mar 14;627(8003):437–444.

Targeted protein degradation via intramolecular bivalent glues. Hsia O, Hinterndorfer M et al. Nature. 2024 Mar 7;627(8002):204–211.

Intranasal SARS-CoV-2 RBD decorated nanoparticle vaccine enhances viral clearance in the Syrian hamster model. Patel DR, Minns AM et al. Microbiol Spectr. 2024 Mar 5;12(3):e0499822.

Structural basis of ribosomal 30S subunit degradation by RNase R. Dimitrova-Paternoga L, Kasvandik S et al. Nature. 2024 Feb 29;626(8001):1133–1140.

Allosteric modulation and G-protein selectivity of the Ca2+-sensing receptor. He F, Wu CG et al. Nature. 2024 Feb 29;626(8001):1141–1148.

Structural basis for sugar perception by Drosophila gustatory receptors. Ma D, Hu M et al. Science. 2024 Feb 23;383(6685):eadj2609.

Convergence of coronary artery disease genes onto endothelial cell programs. Schnitzler GR, Kang H et al. Nature. 2024 Feb 22;626(8000):799-807.

Type III-B CRISPR-Cas cascade of proteolytic cleavages. Steens JA, Bravo JPK et al. Science. 2024 Feb 2;383(6682):512-519.

Template and target-site recognition by human LINE-1 in retrotransposition. Thawani A, Ariza AJF et al. Nature. 2024 Feb 1;626(7997):186–193.


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