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UCSF ChimeraX Citations

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Selected Citations

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.

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.

Structure of the human sodium leak channel NALCN. Kschonsak M, Chua HC et al. Nature. 2020 Nov 12;587(7833):313-318.

The 3.2-Å resolution structure of human mTORC2. Scaiola A, Mangia F et al. Sci Adv. 2020 Nov 6;6(45):eabc1251.

Single-particle cryo-EM at atomic resolution. Nakane T, Kotecha A et al. Nature. 2020 Nov 5;587(7832):152-156.

Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Shaaban M, Chowdhury S, Nolen BJ. Nat Struct Mol Biol. 2020 Nov;27(11):1009-1016.

Molecular architecture of the SARS-CoV-2 virus. Yao H, Song Y et al. Cell. 2020 Oct 29;183(3):730-738.e13.

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors. Cao L, Goreshnik I et al. Science. 2020 Oct 23;370(6515):426-431.

Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM. Soufari H, Parrot C et al. Nat Commun. 2020 Oct 15;11(1):5195.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Turoňová B, Sikora M et al. Science. 2020 Oct 9;370(6513):203-208.

Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation. Grba DN, Hirst J. Nat Struct Mol Biol. 2020 Oct;27(10):892-900.

Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation. McCallum M, Walls AC et al. Nat Struct Mol Biol. 2020 Oct;27(10):942-949.

Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Liu W, Cui Y et al. Nat Microbiol. 2020 Oct;5(10):1285-1298.

The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase. McKenna MJ, Sim SI et al. Science. 2020 Sep 25;369(6511). pii: eabc5809.

90S pre-ribosome transformation into the primordial 40S subunit. Cheng J, Lau B et al. Science. 2020 Sep 18;369(6510):1470-1476.

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Thoms M, Buschauer R et al. Science. 2020 Sep 4;369(6508):1249-1255.

Structure of a human 48S translational initiation complex. Brito Querido J, Sokabe M et al. Science. 2020 Sep 4;369(6508):1220-1227.

Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Ni T, Gerard S et al. Nat Struct Mol Biol. 2020 Sep;27(9):846–854.

Structures of human pannexin 1 reveal ion pathways and mechanism of gating. Ruan Z, Orozco IJ et al. Nature. 2020 Aug 27;584(7822):646-651.

Potent neutralizing antibodies directed to multiple epitopes on SARS-CoV-2 spike. Liu L, Wang P et al. Nature. 2020 Aug 20;584(7821):450-456.

Binding mechanisms of therapeutic antibodies to human CD20. Kumar A, Planchais C et al. Science. 2020 Aug 14;369(6505):793-799.

Structural basis of the activation of a metabotropic GABA receptor. Shaye H, Ishchenko A et al. Nature. 2020 Aug 13;584(7820):298–303.

Structure of human GABAB receptor in an inactive state. Park J, Fu Z et al. Nature. 2020 Aug 13;584(7820):304-309.

Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles. Li Z, Li W et al. Nat Struct Mol Biol. 2020 Aug;27(8):726-734.

Structural insights into differences in G protein activation by family A and family B GPCRs. Hilger D, Kumar KK et al. Science. 2020 Jul 31;369(6503). pii: eaba3373.

In-cell architecture of an actively transcribing-translating expressome. O'Reilly FJ, Xue L et al. Science. 2020 Jul 31;369(6503):554-557.

Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Arragain B, Effantin G et al. Nat Commun. 2020 Jul 17;11(1):3590.

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Pinto D, Park YJ et al. Nature. 2020 Jul 9;583(7815):290-295.

How IGF-II binds to the human type 1 insulin-like growth factor receptor. Xu Y, Kirk NS et al. Structure. 2020 Jul 7;28(7):786-798.e6.

Electromechanical coupling in the hyperpolarization-activated K+ channel KAT1. Clark MD, Contreras GF et al. Nature. 2020 Jul 2;583(7814):145-149.

Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils. Röder C, Kupreichyk T et al. Nat Struct Mol Biol. 2020 Jul;27(7):660-667.

Cryo-EM structure of the human cohesin-NIPBL-DNA complex. Shi Z, Gao H et al. Science. 2020 Jun 26;368(6498):1454-1459.

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation. Tobiasson V, Amunts A. eLife. 2020 Jun 18;9. pii: e59264.

Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Zhang L, Zhao Y et al. Science. 2020 Jun 12;368(6496):1211-1219.

The His-Gly motif of acid-sensing ion channels resides in a reentrant 'loop' implicated in gating and ion selectivity. Yoder N, Gouaux E. eLife. 2020 Jun 4;9. pii: e56527.

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