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UCSF ChimeraX Citations

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Selected Citations

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.

GPCR activation and GRK2 assembly by a biased intracellular agonist. Duan J, Liu H et al. Nature. 2023 Aug 17;620(7974):676–681.

Fanzor is a eukaryotic programmable RNA-guided endonuclease. Saito M, Xu P et al. Nature. 2023 Aug 17;620(7974):660–668.

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.

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.

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

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.

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.

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

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.

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.

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 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.

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

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.

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.

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

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.

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

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

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.

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

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

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

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.

Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Rodrigues-Oliveira T, Wollweber F et al. Nature. 2023 Jan 12;613(7943):332–339.

Integrated intracellular organization and its variations in human iPS cells. Viana MP, Chen J et al. Nature. 2023 Jan 12;613(7943):345–354.

Structure of monkeypox virus DNA polymerase holoenzyme. Peng Q, Xie Y et al. Science. 2023 Jan 6;379(6627):100-105.

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Lugmayr W, Kotov V et al. Nat Protoc. 2023 Jan;18(1):239-264.

Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Xiong Q, Cao L et al. Nature. 2022 Dec 22;612(7941):748–757.

Multifunctional protein A is the only viral protein required for nodavirus RNA replication crown formation. den Boon JA, Zhan H et al. Viruses. 2022 Dec 3;14(12):2711.

ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Ermel UH, Arghittu SM, Frangakis AS. Protein Sci. 2022 Dec;31(12):e4472.

Starting a new chapter on class Ia ribonucleotide reductases. Levitz TS, Drennan CL. Curr Opin Struct Biol. 2022 Dec;77:102489.

Structure determination of inactive-state GPCRs with a universal nanobody. Robertson MJ, Papasergi-Scott MM et al. Nat Struct Mol Biol. 2022 Dec;29(12):1188-1195.

Structural principles of B cell antigen receptor assembly. Dong Y, Pi X et al. Nature. 2022 Dec 1;612(7938):156–161.

Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney. Liu S, Xia X et al. Cell Discov. 2022 Nov 22;8(1):126.

Structure of the human heparan sulfate polymerase complex EXT1-EXT2. Leisico F, Omeiri J et al. Nat Commun. 2022 Nov 19;13(1):7110.

Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Jespersen N, Ehrenbolger K et al. Nat Commun. 2022 Nov 15;13(1):6962.

Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel. Mount J, Maksaev G et al. Nat Commun. 2022 Nov 12;13(1):6904.

Cryo-EM structure of the SEA complex. Tafur L, Hinterndorfer K et al. Nature. 2022 Nov 10;611(7935):399–404.

Structural basis of actin filament assembly and aging. Oosterheert W, Klink BU et al. Nature. 2022 Nov 10;611(7935):374–379.

Molecular glue CELMoD compounds are regulators of cereblon conformation. Watson ER, Novick S et al. Science. 2022 Nov 4;378(6619):549-553.

Mechanism of an intramembrane chaperone for multipass membrane proteins. Smalinskaitė L, Kim MK et al. Nature. 2022 Nov 3;611(7934):161-166.

Dual targeting factors are required for LXG toxin export by the bacterial type VIIb secretion system. Klein TA, Grebenc DW et al. mBio. 2022 Oct 26;13(5):e0213722.

MTCH2 is a mitochondrial outer membrane protein insertase. Guna A, Stevens TA et al. Science. 2022 Oct 21;378(6617):317-322.

Structure of the hepatitis C virus E1E2 glycoprotein complex. Torrents de la Peña A, Sliepen K et al. Science. 2022 Oct 21;378(6617):263-269.

A wheat resistosome defines common principles of immune receptor channels. Förderer A, Li E et al. Nature. 2022 Oct 20;610(7932):532-539.

ScanNet: A web server for structure-based prediction of protein binding sites with geometric deep learning. Tubiana J, Schneidman-Duhovny D, Wolfson HJ. J Mol Biol. 2022 Oct 15;434(19):167758.

Structural basis for directional chitin biosynthesis. Chen W, Cao P et al. Nature. 2022 Oct 13;610(7931):402-408.

Hallucinating symmetric protein assemblies. Wicky BIM, Milles LF et al. Science. 2022 Oct 7;378(6615):56-61.

Visualizing translation dynamics at atomic detail inside a bacterial cell. Xue L, Lenz S et al. Nature. 2022 Oct 6;610(7930):205-211.

Columnar structure of human telomeric chromatin. Soman A, Wong SY et al. Nature. 2022 Sep 29;609(7929):1048-1055.

Activation of the human insulin receptor by non-insulin-related peptides. Kirk NS, Chen Q et al. Nat Commun. 2022 Sep 28;13(1):5695.

Autoantibody mimicry of hormone action at the thyrotropin receptor. Faust B, Billesbølle CB et al. Nature. 2022 Sep 22;609(7928):846-853.

Mechanistic understanding of human SLFN11. Metzner FJ, Wenzl SJ et al. Nat Commun. 2022 Sep 17;13(1):5464.

Organizing structural principles of the IL-17 ligand-receptor axis. Wilson SC, Caveney NA et al. Nature. 2022 Sep 15;609(7927):622-629.

Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration. Wald J, Fahrenkamp D et al. Nature. 2022 Sep 15;609(7927):630-639.

Membranes under the magnetic lens: A dive into the diverse world of membrane protein structures using cryo-EM. Piper SJ, Johnson RM et al. Chem Rev. 2022 Sep 14;122(17):13989-14017.

R-loop formation and conformational activation mechanisms of Cas9. Pacesa M, Loeff L et al. Nature. 2022 Sep 1;609(7925):191-196.

Molecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination. Arvindekar S, Jackman MJ et al. Protein Sci. 2022 Sep;31(9):e4387.

Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA. Kuhle B, Hirschi M et al. Nat Commun. 2022 Aug 30;13(1):5100.

Structural plasticity enables evolution and innovation of RuBisCO assemblies. Liu AK, Pereira JH et al. Sci Adv. 2022 Aug 26;8(34):eadc9440.

Cryo-EM structure of an active bacterial TIR-STING filament complex. Morehouse BR, Yip MCJ et al. Nature. 2022 Aug 25;608(7924):803-807.

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