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UCSF ChimeraX Citations

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Selected Citations

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.

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.

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.

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.

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.

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.

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.

Cryo-EM structure of the human cardiac myosin filament. Dutta D, Nguyen V et al. Nature. 2023 Nov 23;623(7988):853–862.

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.

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.

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.

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.

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.

Structure of an endogenous mycobacterial MCE lipid transporter. Chen J, Fruhauf A et al. Nature. 2023 Aug 10;620(7973):445–452.

Mechanistic snapshots of rhodium-catalyzed acylnitrene transfer reactions. Jung H, Kweon J et al. Science. 2023 Aug 4;381(6657):525-532.

Mechanism of mycobacterial ATP synthase inhibition by squaramides and second generation diarylquinolines. Courbon GM, Palme PR et al. EMBO J. 2023 Aug 1;42(15):e113687.

Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor. Greenhough LA, Liang CC et al. Nature. 2023 Jul 20;619(7970):650–657.

The mechanism of the phage-encoded protein antibiotic from φX174. Orta AK, Riera N et al. Science. 2023 Jul 14;381(6654):eadg9091.

Cooperation between bHLH transcription factors and histones for DNA access. Michael AK, Stoos L et al. Nature. 2023 Jul 13;619(7969):385–393.

Principles of human pre-60S biogenesis. Vanden Broeck A, Klinge S. Science. 2023 Jul 7;381(6653):eadh3892.

Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Liu S, Wang H et al. Science. 2023 Jul 7;381(6653):eadg4725.

Translation dynamics in human cells visualized at high resolution reveal cancer drug action. Xing H, Taniguchi R et al. Science. 2023 Jul 7;381(6653):70-75.

Structural modeling of peptide toxin-ion channel interactions using RosettaDock. Mateos DL, Yarov-Yarovoy V. Proteins. 2023 Jul;91(7):872-889.

Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Degen M, Santos JC et al. Nature. 2023 Jun 29;618(7967):1065-1071.

NAC controls cotranslational N-terminal methionine excision in eukaryotes. Gamerdinger M, Jia M et al. Science. 2023 Jun 23;380(6651):1238-1243.

Structures of the free and capped ends of the actin filament. Carman PJ, Barrie KR et al. Science. 2023 Jun 23;380(6651):1287-1292.

Genome expansion by a CRISPR trimmer-integrase. Wang JY, Tuck OT et al. Nature. 2023 Jun 22;618(7966):855–861.

Axonemal structures reveal mechanoregulatory and disease mechanisms. Walton T, Gui M et al. Nature. 2023 Jun 15;618(7965):625–633.

In situ architecture of the ER-mitochondria encounter structure. Wozny MR, Di Luca A et al. Nature. 2023 Jun 1;618(7963):188–192.

Structural basis of human PRPS2 filaments. Lu GM, Hu HH et al. Cell Biosci. 2023 May 30;13(1):100.

Structural basis of catalytic activation in human splicing. Schmitzová J, Cretu C et al. Nature. 2023 May 25;617(7962):842-850.

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Ikeuchi K, Ivic N et al. Nat Commun. 2023 May 12;14(1):2730.

Structural atlas of a human gut crassvirus. Bayfield OW, Shkoporov AN et al. Nature. 2023 May 11;617(7960):409-416.

Cryptochrome-Timeless structure reveals circadian clock timing mechanisms. Lin C, Feng S et al. Nature. 2023 May 4;617(7959):194–199.

De novo design of protein interactions with learned surface fingerprints. Gainza P, Wehrle S et al. Nature. 2023 May 4;617(7959):176-184.

mRNA decoding in human is kinetically and structurally distinct from bacteria. Holm M, Natchiar SK et al. Nature. 2023 May 4;617(7959):200–207.

Mirusviruses link herpesviruses to giant viruses. Gaïa M, Meng L et al. Nature. 2023 Apr 27;616(7958):783–789.

mRNA recognition and packaging by the human transcription-export complex. Pacheco-Fiallos B, Vorländer MK et al. Nature. 2023 Apr 27;616(7958):828–835.

Structural study of the Cobetia marina bacteriophage 1 (Carin-1) by cryo-EM. d'Acapito A, Roret T et al. J Virol. 2023 Apr 27;97(4):e0024823.

Top-down design of protein architectures with reinforcement learning. Lutz ID, Wang S et al. Science. 2023 Apr 21;380(6642):266-273.

Structural mechanisms for regulation of GSDMB pore-forming activity. Zhong X, Zeng H et al. Nature. 2023 Apr 20;616(7957):598–605.

Sensory specializations drive octopus and squid behaviour. Kang G, Allard CAH et al. Nature. 2023 Apr 13;616(7956):378-383.

Cryo-EM structure of the transposon-associated TnpB enzyme. Nakagawa R, Hirano H et al. Nature. 2023 Apr 13;616(7956):390-397.

Protein complexes in cells by AI-assisted structural proteomics. O'Reilly FJ, Graziadei A et al. Mol Syst Biol. 2023 Apr 12;19(4):e11544.

Basis of the H2AK119 specificity of the Polycomb repressive deubiquitinase. Ge W, Yu C et al. Nature. 2023 Apr 6;616(7955):176–182.

In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex. You X, Zhang X et al. Nature. 2023 Apr 6;616(7955):199–206.

Likelihood-based docking of models into cryo-EM maps. Millán C, McCoy AJ et al. Acta Crystallogr D Struct Biol. 2023 Apr 1;79(Pt 4):281-289.

Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex. Mühleip A, Flygaard RK et al. Nature. 2023 Mar 30;615(7954):934–938.

Structural basis of odorant recognition by a human odorant receptor. Billesbølle CB, de March CA et al. Nature. 2023 Mar 23;615(7953):742–749.

Structures of BIRC6-client complexes provide a mechanism of Smac-mediated release of caspases. Hunkeler M, Jin CY, Fischer ES. Science. 2023 Mar 17;379(6637):1105-1111.

Blebs promote cell survival by assembling oncogenic signalling hubs. Weems AD, Welf ES et al. Nature. 2023 Mar 16;615(7952):517-525.

Coordination of bacterial cell wall and outer membrane biosynthesis. Hummels KR, Berry SP et al. Nature. 2023 Mar 9;615(7951):300–304.

Architecture of chloroplast TOC-TIC translocon supercomplex. Liu H, Li A et al. Nature. 2023 Mar 9;615(7951):349–357.

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Kim SK, Dickinson MS et al. Nat Struct Mol Biol. 2023 Mar;30(3):296-308.

Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter. Fan M, Zhang J et al. Nature. 2023 Feb 23;614(7949):788–793.

Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Mensah MA, Niskanen H et al. Nature. 2023 Feb 16;614(7948):564–571.

Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Cui Z, Napolitano G et al. Nature. 2023 Feb 16;614(7948):572–579.

Visualization of translation and protein biogenesis at the ER membrane. Gemmer M, Chaillet ML et al. Nature. 2023 Feb 2;614(7946):160–167.

Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN. Kinman LF, Powell BM et al. Nat Protoc. 2023 Feb;18(2):319-339.

Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides. Bridges HR, Blaza JN et al. Science. 2023 Jan 27;379(6630):351-357.

Structures of the holo CRISPR RNA-guided transposon integration complex. Park JU, Tsai AW et al. Nature. 2023 Jan 26;613(7945):775-782.

Undecaprenyl phosphate translocases confer conditional microbial fitness. Sit B, Srisuknimit V et al. Nature. 2023 Jan 26;613(7945):721-728.

A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Otsuka S, Tempkin JOB et al. Nature. 2023 Jan 19;613(7944):575–581.

RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2. Bravo JPK, Hallmark T et al. Nature. 2023 Jan 19;613(7944):582–587.


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