UCSF ChimeraX Citations
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Selected Citations
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.
Structure and topography of the synaptic V-ATPase-synaptophysin complex. Wang C, Jiang W et al. Nature. 2024 Jul 25;631(8022):899–904.
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.
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.
Computational design of soluble and functional membrane protein analogues. Goverde CA, Pacesa M et al. Nature. 2024 Jul 11;631(8020):449–458.
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.
Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Zhang S, Sun A et al. Nature. 2024 Jun 13;630(8016):484–492.
Molecular mechanism of choline and ethanolamine transport in humans. Ri K, Weng TH et al. Nature. 2024 Jun 13;630(8016):501–508.
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.
Structures of human γδ T cell receptor-CD3 complex. Xin W, Huang B et al. Nature. 2024 Jun 6;629(8015):222–229.
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.
The intrinsic substrate specificity of the human tyrosine kinome. Yaron-Barir TM, Joughin BA et al. Nature. 2024 May 30;629(8014):1174–1181.
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.
Structural basis of Integrator-dependent RNA polymerase II termination. Fianu I, Ochmann M et al. Nature. 2024 May 2;629(8010):219–227.
Streptomyces umbrella toxin particles block hyphal growth of competing species. Zhao Q, Bertolli S et al. Nature. 2024 May 2;629(8010):165–173.
Molecular insights into capsular polysaccharide secretion. Kuklewicz J, Zimmer J. Nature. 2024 Apr 25;628(8009):901–909.
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.
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.
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.
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.
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.
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 of ribosomal 30S subunit degradation by RNase R. Dimitrova-Paternoga L, Kasvandik S et al. Nature. 2024 Feb 29;626(8001):1133–1140.
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.
Structures, functions and adaptations of the human LINE-1 ORF2 protein. Baldwin ET, van Eeuwen T et al. Nature. 2024 Feb 1;626(7997):194–206.
An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano. Sonani RR, Palmer LK et al. Nat Commun. 2024 Jan 26;15(1):756.
2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein. Ghanim GE, Sekne Z et al. Nat Commun. 2024 Jan 25;15(1):746.
The PfRCR complex bridges malaria parasite and erythrocyte during invasion. Farrell B, Alam N et al. Nature. 2024 Jan 18;625(7995):578–584.
TAF15 amyloid filaments in frontotemporal lobar degeneration. Tetter S, Arseni D et al. Nature. 2024 Jan 11;625(7994):345–351.
mRNA reading frame maintenance during eukaryotic ribosome translocation. Milicevic N, Jenner L et al. Nature. 2024 Jan 11;625(7994):393–400.
Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia. Meng X, Xu C et al. Nat Commun. 2024 Jan 8;15(1):362.
Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors. Maharana J, Sano FK et al. Science. 2024 Jan 5;383(6678):101-108.
Disease-specific tau filaments assemble via polymorphic intermediates. Lövestam S, Li D et al. Nature. 2024 Jan 4;625(7993):119–125.
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Terwilliger TC, Liebschner D et al. Nat Methods. 2024 Jan;21(1):110-116.
Structural visualization of transcription initiation in action. Chen X, Liu W et al. Science. 2023 Dec 22;382(6677):eadi5120.
Ligand recognition and G-protein coupling of trace amine receptor TAAR1. Xu Z, Guo L et al. Nature. 2023 Dec 21;624(7992):672–681.
Recognition of methamphetamine and other amines by trace amine receptor TAAR1. Liu H, Zheng Y et al. Nature. 2023 Dec 21;624(7992):663–671.
Molecular architecture of Salmonella typhimurium virus P22 genome ejection machinery. Iglesias SM, Lokareddy RK et al. J Mol Biol. 2023 Dec 15;435(24):168365.
Structural insights into cytokine cleavage by inflammatory caspase-4. Devant P, Dong Y et al. Nature. 2023 Dec 14;624(7991):451–459.
Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Muir KW, Batters C et al. Science. 2023 Dec 8;382(6675):1184-1190.
The social and structural architecture of the yeast protein interactome. Michaelis AC, Brunner AD et al. Nature. 2023 Dec 7;624(7990):192–200.
The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Braxton JR, Altobelli CR et al. Nat Struct Mol Biol. 2023 Dec;30(12):2009-2019.
PTM-Psi: A python package to facilitate the computational investigation of post-translational modification on protein structures and their impacts on dynamics and functions. Mejia-Rodriguez D, Kim H et al. Protein Sci. 2023 Dec;32(12):e4822.
Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Dam KA, Fan C et al. Nature. 2023 Nov 30;623(7989):1017-1025.
HIV-1 Env trimers asymmetrically engage CD4 receptors in membranes. Li W, Qin Z et al. Nature. 2023 Nov 30;623(7989):1026-1033.
Structure of the native myosin filament in the relaxed cardiac sarcomere. Tamborrini D, Wang Z et al. Nature. 2023 Nov 23;623(7988):863–871.
Cryo-EM structure of the human cardiac myosin filament. Dutta D, Nguyen V et al. Nature. 2023 Nov 23;623(7988):853–862.
Autoregulatory control of mitochondrial glutathione homeostasis. Liu Y, Liu S et al. Science. 2023 Nov 17;382(6672):eadf4154.
Rapid bacteria-phage coevolution drives the emergence of multiscale networks. Borin JM, Lee JJ et al. Science. 2023 Nov 10;382(6671):674-678.
Structure of LRRK1 and mechanisms of autoinhibition and activation. Reimer JM, Dickey AM et al. Nat Struct Mol Biol. 2023 Nov;30(11):1735-1745.
Structure reveals why genome folding is necessary for site-specific integration of foreign DNA into CRISPR arrays. Santiago-Frangos A, Henriques WS et al. Nat Struct Mol Biol. 2023 Nov;30(11):1675-1685.
OPUS-DSD: deep structural disentanglement for cryo-EM single-particle analysis. Luo Z, Ni F et al. Nat Methods. 2023 Nov;20(11):1729-1738.
Spatial atlas of the mouse central nervous system at molecular resolution. Shi H, He Y et al. Nature. 2023 Oct 19;622(7983):552–561.
Clustering predicted structures at the scale of the known protein universe. Barrio-Hernandez I, Yeo J et al. Nature. 2023 Oct 19;622(7983):637–645.
piRNA processing by a trimeric Schlafen-domain nuclease. Podvalnaya N, Bronkhorst AW et al. Nature. 2023 Oct 12;622(7982):402–409.
PIM1 controls GBP1 activity to limit self-damage and to guard against pathogen infection. Fisch D, Pfleiderer MM et al. Science. 2023 Oct 6;382(6666):eadg2253.
Parkinson's disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella. Lian H, Park D et al. Nat Microbiol. 2023 Oct;8(10):1880-1895.
Direct measurements of biomolecular electrostatics through experiments. Iwahara J, Pettitt BM, Yu B. Curr Opin Struct Biol. 2023 Oct;82:102680.
DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans. Xia Y, Sonneville R et al. Science. 2023 Sep 22;381(6664):eadi4932.
Central role of Tim17 in mitochondrial presequence protein translocation. Fielden LF, Busch JD et al. Nature. 2023 Sep 21;621(7979):627–634.
Conserved class B GPCR activation by a biased intracellular agonist. Zhao LH, He Q et al. Nature. 2023 Sep 21;621(7979):635–641.
Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation. Juyoux P, Galdadas I et al. Science. 2023 Sep 15;381(6663):1217-1225.
Oligomerization-mediated activation of a short prokaryotic Argonaute. Shen Z, Yang XY et al. Nature. 2023 Sep 7;621(7977):154–161.
Signal peptide mimicry primes Sec61 for client-selective inhibition. Rehan S, Tranter D et al. Nat Chem Biol. 2023 Sep;19(9):1054-1062.
De novo design of protein structure and function with RFdiffusion. Watson JL, Juergens D et al. Nature. 2023 Aug 31;620(7976):1089–1100.
Structural mechanism of mitochondrial membrane remodelling by human OPA1. von der Malsburg A, Sapp GM et al. Nature. 2023 Aug 31;620(7976):1101–1108.
TDP-43 forms amyloid filaments with a distinct fold in type A FTLD-TDP. Arseni D, Chen R et al. Nature. 2023 Aug 24;620(7975):898–903.
Fanzor is a eukaryotic programmable RNA-guided endonuclease. Saito M, Xu P et al. Nature. 2023 Aug 17;620(7974):660–668.
GPCR activation and GRK2 assembly by a biased intracellular agonist. Duan J, Liu H et al. Nature. 2023 Aug 17;620(7974):676–681.