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UCSF ChimeraX Citations

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Selected Citations

The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies. Swanson K, Wu W et al. Nature. 2025 Oct 16;646(8085):716–723.

“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling. Tao CL, Tian CL et al. Science. 2025 Oct 16;390(6770):eads7954.

Structural basis for the dynamic regulation of mTORC1 by amino acids. Valenstein ML, Wranik M et al. Nature. 2025 Oct 9;646(8084):493–500.

One-shot design of functional protein binders with BindCraft. Pacesa M, Nickel L et al. Nature. 2025 Oct 9;646(8084):483–492.

A nanobody specific to prefusion glycoprotein B neutralizes HSV-1 and HSV-2. Vollmer B, Ebel H et al. Nature. 2025 Oct 9;646(8084):433–441.

A novel bacterial protein family that catalyses nitrous oxide reduction. He G, Wang W et al. Nature. 2025 Oct 2;646(8083):152–160.

Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases. Vinayagam D, Sitsel O et al. Nature. 2025 Oct 2;646(8083):236–245.

Structural basis of fast N-type inactivation in Kv channels. Tan XF, Fernández-Mariño AI et al. Nature. 2025 Sep 25;645(8082):1081–1089.

Subtype-specific structural features of the hearing loss-associated human P2X2 receptor. Westermann FG, Oken AC et al. Proc Natl Acad Sci USA. 2025 Sep 16;122(37):e2417753122.

Molecular exaptation by the integrin αI domain. Hollis JA, Chan MC et al. Sci Adv. 2025 Sep 12;11(37):eadx9567.

Architecture, dynamics and biogenesis of GluA3 AMPA glutamate receptors. Pokharna A, Stockwell I et al. Nature. 2025 Sep 11;645(8080):535–543.

Epithelial cell membrane perforation induces allergic airway inflammation. Shi K, Lv Y et al. Nature. 2025 Sep 11;645(8080):475–483.

Cryo-EM structure of endogenous Plasmodium falciparum Pfs230 and Pfs48/45 fertilization complex. Dietrich MH, Chmielewski J et al. Science. 2025 Sep 11;389(6765):eady0241.

Loss of FCoV-23 spike domain 0 enhances fusogenicity and entry kinetics. Tortorici MA, Choi A et al. Nature. 2025 Sep 4;645(8079):235–243.

ArtiaX: geometric models, camera paths and image processing tools. Roth P, Ermel UH et al. J Struct Biol. 2025 Sep;217(3):108215.

Cryo-EM structure of a natural RNA nanocage. Ling X, Golovenko D et al. Nature. 2025 Aug 28;644(8078):1107–1115.

Disassembly activates Retron-Septu for antiphage defense. Wang C, Rish AD et al. Science. 2025 Aug 21;389(6762):eadv3344.

Cryo-EM identifies F-ENA of Bacillus thuringiensis as a widespread family of endospore appendages across Firmicutes. Sleutel M, Sogues A et al. Nat Commun. 2025 Aug 16;16(1):7652.

Electron flow in hydrogenotrophic methanogens under nickel limitation. Nomura S, San Segundo-Acosta P et al. Nature. 2025 Aug 14;644(8076):490-496.

Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme. Andorfer MC, Levitz TS et al. Proc Natl Acad Sci USA. 2025 Aug 12;122(32):e2510389122.

Structural basis for postfusion-specific binding to the respiratory syncytial virus F protein by the canonical antigenic site I antibody 131-2a. Peng W, Šiborová M et al. ACS Infect Dis. 2025 Aug 8;11(8):2357-2366.

Cryogenic electron tomography reveals helical organization of lipoprotein lipase in storage vesicles. Gunn KH, Wheless A et al. Sci Adv. 2025 Aug 8;11(32):eadx8711.

Interactions between TTYH2 and APOE facilitate endosomal lipid transfer. Sukalskaia A, Karner A et al. Nature. 2025 Aug 7;644(8075):273–279.

Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1. Jing D, Kong F et al. Proc Natl Acad Sci USA. 2025 Aug 5;122(31):e2513424122.

Structure of the microtubule-anchoring factor NEDD1 bound to the γ-tubulin ring complex. Muñoz-Hernández H, Xu Y et al. J Cell Biol. 2025 Aug 4;224(8):e202410206.

PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures. Vallat B, Webb BM et al. J Mol Biol. 2025 Aug 1;437(15):168963.

Protein-primed homopolymer synthesis by an antiviral reverse transcriptase. Tang S, Žedaveinytė R et al. Nature. 2025 Jul 31;643(8074):1352–1362.

SP140-RESIST pathway regulates interferon mRNA stability and antiviral immunity. Witt KC, Dziulko A et al. Nature. 2025 Jul 31;643(8074):1372–1380.

Precise targeting of HIV broadly neutralizing antibody precursors in humans. Caniels TG, Prabhakaran M et al. Science. 2025 Jul 31;389(6759):eadv5572.

Molecular basis of SIFI activity in the integrated stress response. Yang Z, Haakonsen DL et al. Nature. 2025 Jul 24;643(8073):1117–1126.

Naturally ornate RNA-only complexes revealed by cryo-EM. Kretsch RC, Wu Y et al. Nature. 2025 Jul 24;643(8073):1135–1142.

Probing condensate microenvironments with a micropeptide killswitch. Zhang Y, Stöppelkamp I et al. Nature. 2025 Jul 24;643(8073):1107–1116.

Stepwise ATP translocation into the endoplasmic reticulum by human SLC35B1. Gulati A, Ahn DH et al. Nature. 2025 Jul 17;(8072):855–864.

Atomic-resolution structure of a chimeric Powassan tick-borne flavivirus. Das S, Narayanan A et al. Sci Adv. 2025 Jul 11;11(28):eadw7700.

Custom CRISPR-Cas9 PAM variants via scalable engineering and machine learning. Silverstein RA, Kim N et al. Nature. 2025 Jul 10;643(8071):539-550.

Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated dimerization. Balch S, Sekne Z et al. Science. 2025 Jul 10;389(6756):eadr5817.

MIC: A deep learning tool for assigning ions and waters in cryo-EM and crystal structures. Shub L, Liu W et al. Nat Commun. 2025 Jul 4;16(1):6182.

Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor. Chen Q, Schafer CT et al. Nature. 2025 Jul 3;643(8070):280–287.

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression. Bianchi D, Borza R et al. Science. 2025 Jul 3;389(6755):eadv2861.

In situ structure of a bacterial flagellar motor at subnanometre resolution reveals adaptations for increased torque. Drobnič T, Cohen EJ et al. Nat Microbiol. 2025 Jul;10(7):1723-1740.

Chromosome end protection by RAP1-mediated inhibition of DNA-PK. Eickhoff P, Sonmez C et al. Nature. 2025 Jun 26;642(8069):1090–1096.

Structure of the ATP-driven methyl-coenzyme M reductase activation complex. Ramírez-Amador F, Paul S et al. Nature. 2025 Jun 19;642(8068):814–821.

Lewy-MSA hybrid fold drives distinct neuronal α-synuclein pathology. Enomoto M, Martinez-Valbuena I et al. Commun Biol. 2025 Jun 16;8(1):929.

Small molecules restore mutant mitochondrial DNA polymerase activity. Valenzuela S, Zhu X et al. Nature. 2025 Jun 12;642(8067):501–507.

PLA2G15 is a BMP hydrolase and its targeting ameliorates lysosomal disease. Nyame K, Xiong J et al. Nature. 2025 Jun 12;642(8067):474–483.

Complex water networks visualized by cryogenic electron microscopy of RNA. Kretsch RC, Li S et al. Nature. 2025 Jun 5;642(8066):250–259.

Structural basis for target DNA cleavage and guide RNA processing by CRISPR-Casλ2. Omura SN, Alfonse LE et al. Commun Biol. 2025 Jun 5;8(1):876.

BRAF oncogenic mutants evade autoinhibition through a common mechanism. Lavoie H, Jin T et al. Science. 2025 May 29;388(6750):eadp2742.

MFSD6 is an entry receptor for enterovirus D68. Varanese L, Xu L et al. Nature. 2025 May 29;641(8065):1268–1275.

BMAL1-HIF2A heterodimer modulates circadian variations of myocardial injury. Ruan W, Li T et al. Nature. 2025 May 22;641(8064):1017-1028.

Glutamate gating of AMPA-subtype iGluRs at physiological temperatures. Kumar Mondal A, Carrillo E et al. Nature. 2025 May 15;641(8063):788–796.

Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis. Peng R, Xu X et al. Science. 2025 May 15;388(6748):eadq7597.

Structure of the human TWIK-2 potassium channel and its inhibition by pimozide. Khanra NK, Wang C et al. Proc Natl Acad Sci USA. 2025 May 13;122(19):e2425709122.

High-resolution characterization of ex vivo AAT polymers by solution-state NMR spectroscopy. Lowen SM, Waudby CA et al. Sci Adv. 2025 May 9;11(19):eadu7064.

The RAD52 double-ring remodels replication forks restricting fork reversal. Honda M, Razzaghi M et al. Nature. 2025 May 8;641(8062):512–519.

Snapshots of acyl carrier protein shuttling in human fatty acid synthase. Schultz K, Costa-Pinheiro P et al. Nature. 2025 May 8;641(8062):520–528.

Structural dynamics of human fatty acid synthase in the condensing cycle. Choi W, Li C et al. Nature. 2025 May 8;641(8062):529–536.

Structural dynamics of DNA unwinding by a replicative helicase. Shahid T, Danazumi AU et al. Nature. 2025 May 1;641(8061):240–249.

Cryo-EM reveals mechanisms of natural RNA multivalency. Wang L, Xie J et al. Science. 2025 May 1;388(6746):545-550.

Base-modified nucleotides mediate immune signaling in bacteria. Zeng Z, Hu Z et al. Science. 2025 Apr 25;388(6745):eads6055.

Structural mechanism of LINE-1 target-primed reverse transcription. Ghanim GE, Hu H et al. Science. 2025 Apr 25;388(6745):eads8412.

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology. Sanguankiattichai N, Chandrasekar B et al. Science. 2025 Apr 18;388(6744):297-303.

Structure of human PINK1 at a mitochondrial TOM-VDAC array. Callegari S, Kirk NS et al. Science. 2025 Apr 18;388(6744):303-310.

Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Cook ASI, Chen M et al. Science. 2025 Apr 11;388(6743):eadl3787.

A coronavirus assembly inhibitor that targets the viral membrane protein. Laporte M, Jochmans D et al. Nature. 2025 Apr 10;640(8058):514–523.

Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import. Chang YT, Barad BA et al. J Cell Biol. 2025 Apr 7;224(4):e202407110.

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses. Castiglione GM, Chen X et al. Science. 2025 Mar 28;387(6741):eadr8589.

Structural basis for the pore-forming activity of a complement-like toxin. Johnstone BA, Christie MP et al. Sci Adv. 2025 Mar 28;11(13):eadt2127.

Structure and mechanism of the Zorya anti-phage defence system. Hu H, Popp PF et al. Nature. 2025 Mar 27;639(8056):1093-1101.

Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids. Šolinc G, Srnko M et al. Nat Commun. 2025 Mar 26;16(1):2972.

Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland. Almeida GMF, Arriaga I et al. eLife. 2025 Mar 25;13:RP103492.

In-cell architecture of the mitochondrial respiratory chain. Waltz F, Righetto RD et al. Science. 2025 Mar 21;387(6740):1296-1301.

Structure and mechanism of vitamin-K-dependent γ-glutamyl carboxylase. Wang R, Chen B et al. Nature. 2025 Mar 20;639(8055):808–815.

Molecular basis of vitamin-K-driven γ-carboxylation at the membrane interface. Cao Q, Ammerman A et al. Nature. 2025 Mar 20;639(8055):816–824.

Evolutionary adaptations of doublet microtubules in trypanosomatid parasites. Doran MH, Niu Q et al. Science. 2025 Mar 14;387(6739):eadr5507.

Tunneling nanotube-like structures regulate distant cellular interactions during heart formation. Miao L, Lu Y et al. Science. 2025 Mar 14;387(6739):eadd3417.

Targeting protein-ligand neosurfaces with a generalizable deep learning tool. Marchand A, Buckley S et al. Nature. 2025 Mar 13;639(8054):522–531.

Structural insights into RNA cleavage by PIWI Argonaute. Li Z, Xu Q et al. Nature. 2025 Mar 6;639(8053):250–259.

High-resolution structures of Myosin-IC reveal a unique actin-binding orientation, ADP release pathway, and power stroke trajectory. Chavali SS, Carman PJ et al. Proc Natl Acad Sci USA. 2025 Mar 4;122(9):e2415457122.

Plant pathogenic fungi hijack phosphate signaling with conserved enzymatic effectors. McCombe CL, Wegner A et al. Science. 2025 Feb 28;387(6737):955-962.

Antiviral signaling of a type III CRISPR-associated deaminase. Li Y, Li Z et al. Science. 2025 Feb 21;387(6736):eadr0393.

The structure of apolipoprotein B100 from human low-density lipoprotein. Berndsen ZT, Cassidy CK. Nature. 2025 Feb 20;638(8051):836–843.

Passage of the HIV capsid cracks the nuclear pore. Kreysing JP, Heidari M et al. Cell. 2025 Feb 20;188(4):930-943.e21.

Bat genomes illuminate adaptations to viral tolerance and disease resistance. Morales AE, Dong Y et al. Nature. 2025 Feb 13;638(8050):449–458.

C-terminal amides mark proteins for degradation via SCF-FBXO31. Muhar MF, Farnung J et al. Nature. 2025 Feb 13;638(8050):519–527.

Resolving native GABAA receptor structures from the human brain. Zhou J, Noviello CM et al. Nature. 2025 Feb 13;638(8050):562–568.

Four-component protein nanocages designed by programmed symmetry breaking. Lee S, Kibler RD et al. Nature. 2025 Feb 13;638(8050):546–552.

Structural basis of inhibition of human NaV1.8 by the tarantula venom peptide Protoxin-I. Neumann B, McCarthy S, Gonen S. Nat Commun. 2025 Feb 7;16(1):1459.

Crosslinking intermodular condensation in non-ribosomal peptide biosynthesis. Heberlig GW, La Clair JJ, Burkart MD. Nature. 2025 Feb 6;638(8049):261–269.

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Yin MD, Lemaire ON et al. Science. 2025 Jan 31;387(6733):498-504.

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription. Markert JW, Soffers JH, Farnung L. Science. 2025 Jan 31;387(6733):528-533.

Novel lineage of anelloviruses with large genomes identified in dolphins. De Koch MD, Krupovic M et al. J Virol. 2025 Jan 31;99(1):e0137024.

Native DGC structure rationalizes muscular dystrophy-causing mutations. Liu S, Su T et al. Nature. 2025 Jan 30;637(8048):1261–1271.

Structural diversity of axonemes across mammalian motile cilia. Leung MR, Sun C et al. Nature. 2025 Jan 30;637(8048):1170-1177.

Conformational protection of molybdenum nitrogenase by Shethna protein II. Franke P, Freiberger S et al. Nature. 2025 Jan 23;637(8047):998–1004.

In situ analysis reveals the TRiC duty cycle and PDCD5 as an open-state cofactor. Xing H, Rosenkranz RRE et al. Nature. 2025 Jan 23;637(8047):983–990.

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. Soczek KM, Cofsky JC et al. Nucleic Acids Res. 2025 Jan 11;53(2):gkae1192.

Tracking transcription-translation coupling in real time. Qureshi NS, Duss O. Nature. 2025 Jan 9;637(8045):487–495.

Autoinhibition of dimeric NINJ1 prevents plasma membrane rupture. Pourmal S, Truong ME et al. Nature. 2025 Jan 9;637(8045):446–452.

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation. Stadnicki EJ, Ludewig H et al. Proc Natl Acad Sci USA. 2025 Jan 7;122(1):e2415150122.


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