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UCSF ChimeraX Citations

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Selected Citations

Cryo-EM structures of amyloid-β 42 filaments from human brains. Yang Y, Arseni D et al. Science. 2022 Jan 14;375(6577):167-172.

Structural basis of branch site recognition by the human spliceosome. Tholen J, Razew M et al. Science. 2022 Jan 7;375(6576):50-57.

Structure of pathological TDP-43 filaments from ALS with FTLD. Arseni D, Hasegawa M et al. Nature. 2022 Jan 6;601(7891):139–143.

Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. McCallum M, Walls AC et al. Science. 2021 Dec 24;374(6575):1621-1626.

A conserved mechanism for regulating replisome disassembly in eukaryotes. Jenkyn-Bedford M, Jones ML et al. Nature. 2021 Dec 23;600(7890):743–747.

A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC. Lewis AJO, Hegde RS. BMC Biol. 2021 Dec 15;19(1):266.

Nuclear pores dilate and constrict in cellulo. Zimmerli CE, Allegretti M et al. Science. 2021 Dec 10;374(6573):eabd9776.

Structural insights into Ubr1-mediated N-degron polyubiquitination. Pan M, Zheng Q et al. Nature. 2021 Dec 9;600(7888):334–338.

How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Waltz F, Salinas-Giegé T et al. Nat Commun. 2021 Dec 9;12(1):7176.

Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. Mast FD, Fridy PC et al. eLife. 2021 Dec 7;10:e73027.

Mechanism for the activation of the anaplastic lymphoma kinase receptor. Reshetnyak AV, Rossi P et al. Nature. 2021 Dec 2;600(7887):153–157.

Structure and desensitization of AMPA receptor complexes with type II TARP γ5 and GSG1L. Klykov O, Gangwar SP et al. Mol Cell. 2021 Dec 2;81(23):4771-4783.e7.

Nanometer-resolution in situ structure of the SARS-CoV-2 postfusion spike protein. Tai L, Zhu G et al. Proc Natl Acad Sci USA. 2021 Nov 30;118(48):e2112703118.

Molecular architecture of black widow spider neurotoxins. Chen M, Blum D et al. Nat Commun. 2021 Nov 29;12(1):6956.

Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding. Solon AL, Tan Z et al. Sci Adv. 2021 Nov 19;7(47):eabj9812.

Structural mechanisms for gating and ion selectivity of the human polyamine transporter ATP13A2. Tillinghast J, Drury S et al. Mol Cell. 2021 Nov 18;81(22):4650-4662.e4.

Architecture and assembly mechanism of native glycine receptors. Zhu H, Gouaux E. Nature. 2021 Nov 18;599(7885):513-517.

Target site selection and remodelling by type V CRISPR-transposon systems. Querques I, Schmitz M et al. Nature. 2021 Nov 18;599(7885):497-502.

The structure of neurofibromin isoform 2 reveals different functional states. Naschberger A, Baradaran R et al. Nature. 2021 Nov 11;599(7884):315-319.

Cryo-EM structures of PI3Kα reveal conformational changes during inhibition and activation. Liu X, Yang S et al. Proc Natl Acad Sci USA. 2021 Nov 9;118(45):e2109327118.

Structural features of nucleosomes in interphase and metaphase chromosomes. Arimura Y, Shih RM et al. Mol Cell. 2021 Nov 4;81(21):4377-4397.e12.

Distinct allosteric mechanisms of first-generation MsbA inhibitors. Thélot FA, Zhang W et al. Science. 2021 Oct 29;374(6567):580-585.

Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor. Basore K, Ma H et al. Nature. 2021 Oct 28;598(7882):672–676.

Structures of full-length glycoprotein hormone receptor signalling complexes. Duan J, Xu P et al. Nature. 2021 Oct 28;598(7882):688–692.

Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Errico JM, Zhao H et al. Cell Rep. 2021 Oct 26;37(4):109881.

Structure of a human replisome shows the organisation and interactions of a DNA replication machine. Jones ML, Baris Y et al. EMBO J. 2021 Oct 25:e108819.

Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study. Hastie KM, Li H et al. Science. 2021 Oct 22;374(6566):eabh2315.

Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies. Lempp FA, Soriaga LB et al. Nature. 2021 Oct 14;598(7880):342-347.

Reconstitution of an intact clock reveals mechanisms of circadian timekeeping. Chavan AG, Swan JA et al. Science. 2021 Oct 8;374(6564):eabd4453.

Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Rao Q, Han L et al. Nat Struct Mol Biol. 2021 Oct;28(10):799-810.

Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Zhang K, Julius D, Cheng Y. Cell. 2021 Sep 30;184(20):5138-5150.e12.

Structure of human cytomegalovirus virion reveals host tRNA binding to capsid-associated tegument protein pp150. Liu YT, Strugatsky D et al. Nat Commun. 2021 Sep 17;12(1):5513.

SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems. Schaefer AJ, Ingman VM, Wheeler SE. J Comput Chem. 2021 Sep 15;42(24):1750-1754.

Regulation of human mTOR complexes by DEPTOR. Wälchli M, Berneiser K et al. eLife. 2021 Sep 14;10:e70871.

Nucleolar maturation of the human small subunit processome. Singh S, Vanden Broeck A et al. Science. 2021 Sep 10;373(6560):eabj5338.

Structural basis for piRNA targeting. Anzelon TA, Chowdhury S et al. Nature. 2021 Sep 9;597(7875):285-289.

Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Liu C, Shi W et al. Science. 2021 Sep 3;373(6559):1142-1146.

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Starr TN, Czudnochowski N et al. Nature. 2021 Sep 2;597(7874):97-102.

Broad sarbecovirus neutralization by a human monoclonal antibody. Tortorici MA, Czudnochowski N et al. Nature. 2021 Sep 2;597(7874):103-108.

A topological switch in CFTR modulates channel activity and sensitivity to unfolding. Scholl D, Sigoillot M et al. Nat Chem Biol. 2021 Sep;17(9):989-997.

Accurate prediction of protein structures and interactions using a three-track neural network. Baek M, DiMaio F et al. Science. 2021 Aug 20;373(6557):871-876.

Structural basis for target site selection in RNA-guided DNA transposition systems. Park JU, Tsai AW et al. Science. 2021 Aug 13;373(6556):768-774.

Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Wang L, Zhou T et al. Science. 2021 Aug 13;373(6556):eabh1766.

Structural insights into how Prp5 proofreads the pre-mRNA branch site. Zhang Z, Rigo N et al. Nature. 2021 Aug 12;596(7871):296-300.

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. McCallum M, Bassi J et al. Science. 2021 Aug 6;373(6555):648-654.

Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Gobeil SM, Janowska K et al. Science. 2021 Aug 6;373(6555):eabi6226.

Building better barrels – β-barrel biogenesis and insertion in bacteria and mitochondria. Diederichs KA, Buchanan SK, Botos I. J Mol Biol. 2021 Aug 6;433(16):166894.

Structural basis of human separase regulation by securin and CDK1-cyclin B1. Yu J, Raia P et al. Nature. 2021 Aug 5;596(7870):138-142.

Structural basis of early translocation events on the ribosome. Rundlet EJ, Holm M et al. Nature. 2021 Jul 29;595(7869):741-745.

CryoEM structure of the Nipah virus nucleocapsid assembly. Ker DS, Jenkins HT et al. PLoS Pathog. 2021 Jul 16;17(7):e1009740.

G-protein activation by a metabotropic glutamate receptor. Seven AB, Barros-Álvarez X et al. Nature. 2021 Jul 15;595(7867):450-454.

Folding of cohesin's coiled coil is important for Scc2/4-induced association with chromosomes. Petela NJ, Gonzalez Llamazares A et al. eLife. 2021 Jul 14;10:e67268.

Structure and dynamics of semaglutide- and taspoglutide-bound GLP-1R-Gs complexes. Zhang X, Belousoff MJ et al. Cell Rep. 2021 Jul 13;36(2):109374.

Nuclear cGAS: guard or prisoner? de Oliveira Mann CC, Hopfner KP. EMBO J. 2021 Jul 12:e108293.

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity. Gupta TK, Klumpe S et al. Cell. 2021 Jul 8;184(14):3643-3659.e23.

Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Xu J, Xu K et al. Nature. 2021 Jul 8;595(7866):278-282.

Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. Kern DM, Sorum B et al. Nat Struct Mol Biol. 2021 Jul;28:573–582.

Structural basis of GABAB receptor-Gi protein coupling. Shen C, Mao C et al. Nature. 2021 Jun 24;594(7864):594-598.

The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6. Feng X, Noguchi Y et al. Nat Commun. 2021 Jun 23;12(1):3883.

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Bhatt PR, Scaiola A et al. Science. 2021 Jun 18;372(6548):1306-1313.

Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT. Jiang Y, Benz TL, Long SB. Science. 2021 Jun 11;372(6547):1215-1219.

Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia. Asarnow D, Wang B et al. Cell. 2021 Jun 10;184(12):3192-3204.e16.

Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Voss WN, Hou YJ et al. Science. 2021 Jun 4;372(6546):1108-1112.

Structural insights into the cross-neutralization of SARS-CoV and SARS-CoV-2 by the human monoclonal antibody 47D11. Fedry J, Hurdiss DL et al. Sci Adv. 2021 Jun 2;7(23):eabf5632.

Structure and dynamics of a mycobacterial type VII secretion system. Bunduc CM, Fahrenkamp D et al. Nature. 2021 May 20;593(7859):445-448.

Structure of human telomerase holoenzyme with bound telomeric DNA. Ghanim GE, Fountain AJ et al. Nature. 2021 May 20;593(7859):449-453.

Cork-in-bottle mechanism of inhibitor binding to mammalian complex I. Chung I, Serreli R et al. Sci Adv. 2021 May 14;7(20):eabg4000.

Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins. Dang HV, Cross RW et al. Nat Struct Mol Biol. 2021 May;28(5):426-434.

Structural insights into preinitiation complex assembly on core promoters. Chen X, Qi Y et al. Science. 2021 Apr 30;372(6541):eaba8490.

Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Noviello CM, Gharpure A et al. Cell. 2021 Apr 15;184(8):2121-2134.e13.

Structural insights into the lipid and ligand regulation of serotonin receptors. Xu P, Huang S et al. Nature. 2021 Apr 15;592(7854):469-473.

Sweet taste of heavy water. Ben Abu N, Mason PE et al. Commun Biol. 2021 Apr 6;4(1):440.

Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Pochopien AA, Beckert B et al. Proc Natl Acad Sci USA. 2021 Apr 6;118(14):e2022756118.

Structure of the human Mediator-bound transcription preinitiation complex. Abdella R, Talyzina A et al. Science. 2021 Apr 2;372(6537):52-56.

Adaptive Cartesian and torsional restraints for interactive model rebuilding. Croll TI, Read RJ. Acta Crystallogr D Struct Biol. 2021 Apr 1;77(Pt 4):438-446.

Structure-based decoupling of the pro- and anti-inflammatory functions of interleukin-10. Saxton RA, Tsutsumi N et al. Science. 2021 Mar 19;371(6535):eabc8433.

Architecture and structural dynamics of the heteromeric GluK2/K5 kainate receptor. Khanra N, Brown PM et al. eLife. 2021 Mar 16;10:e66097.

Improving SARS-CoV-2 structures: Peer review by early coordinate release. Croll TI, Williams CJ et al. Biophys J. 2021 Mar 16;120(6):1085-1096.

Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation. Miletic S, Fahrenkamp D et al. Nat Commun. 2021 Mar 9;12(1):1546.

Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Yang Y, Harris KA et al. Proc Natl Acad Sci USA. 2021 Mar 2;118(9):e2020393118.

Molecular architecture of the endocytic TPLATE complex. Yperman K, Wang J et al. Sci Adv. 2021 Feb 26;7(9):eabe7999.

Shulin packages axonemal outer dynein arms for ciliary targeting. Mali GR, Ali FA et al. Science. 2021 Feb 26;371(6532):910-916.

Mechanism of membrane-tethered mitochondrial protein synthesis. Itoh Y, Andréll J et al. Science. 2021 Feb 19;371(6531):846-849.

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Koenig PA, Das H et al. Science. 2021 Feb 12;371(6530):eabe6230.

Mitochondrial sorting and assembly machinery operates by β-barrel switching. Takeda H, Tsutsumi A et al. Nature. 2021 Feb 4;590(7844):163-169.

Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Hennell James R, Deme JC et al. Nat Microbiol. 2021 Feb;6(2):221-233.

Structures of the glucocorticoid-bound adhesion receptor GPR97-G(o) complex. Ping YQ, Mao C et al. Nature. 2021 Jan 28;589(7843):620-626.

Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Bai R, Wan R et al. Science. 2021 Jan 8;371(6525):eabe8863.

Structure of the class D GPCR Ste2 dimer coupled to two G proteins. Velazhahan V, Ma N et al. Nature. 2021 Jan 7;589(7840):148-153.

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline. Guo H, Courbon GM et al. Nature. 2021 Jan 7;589(7840):143-147.

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure. Saltzberg DJ, Viswanath S et al. Protein Sci. 2021 Jan;30(1):250-261.

Causes and consequences of RNA polymerase II stalling during transcript elongation. Noe Gonzalez M, Blears D, Svejstrup JQ. Nat Rev Mol Cell Biol. 2021 Jan;22(1):3-21.

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Xiang Y, Nambulli S et al. Science. 2020 Dec 18;370(6523):1479-1484.

An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Schoof M, Faust B et al. Science. 2020 Dec 18;370(6523):1473-1479.

Genetic interaction mapping informs integrative structure determination of protein complexes. Braberg H, Echeverria I et al. Science. 2020 Dec 11;370(6522):eaaz4910.

Structures and pH-sensing mechanism of the proton-activated chloride channel. Ruan Z, Osei-Owusu J et al. Nature. 2020 Dec 10;588(7837):350-354.

Structure of the activated ROQ1 resistosome directly recognizing the pathogen effector XopQ. Martin R, Qi T et al. Science. 2020 Dec 4;370(6521):eabd9993.

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Gordon DE, Hiatt J et al. Science. 2020 Dec 4;370(6521):eabe9403.

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate. Bangaru S, Ozorowski G et al. Science. 2020 Nov 27;370(6520):1089-1094.

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Tortorici MA, Beltramello M et al. Science. 2020 Nov 20;370(6519):950-957.

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