home overview research resources outreach & training outreach & training visitors center visitors center search search

Quick Links

Chimera Search

Google™ Search

Citations (partial list)

A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation. Gayathri P, Fujii T et al. Science. 2012 Dec 7;338(6112):1334-7.

A global comparison of the human and T. brucei degradomes gives insights about possible parasite drug targets. Mashiyama ST, Koupparis K et al. PLoS Negl Trop Dis. 2012 Dec 6;6(12): e1942.

MP2 energy and density for large molecular systems with internal error control using the Divide-Expand-Consolidate scheme. Kristensen K, Høyvik IM et al. Phys Chem Chem Phys. 2012 Dec 5;14(45):15706-14.

Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Greber BJ, Boehringer D et al. Nat Struct Mol Biol. 2012 Nov 11;19(12):1228-33.

Coagulation factor X activates innate immunity to human species C adenovirus. Doronin K, Flatt JW et al. Science. 2012 Nov 9;338(6108):795-8.

Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures. Wu L, Chai D et al. PLoS One. 2012 Nov 9;7(11):e49225.

A virus-like particle that elicits cross-reactive antibodies to the conserved stem of influenza virus hemagglutinin. Schneemann A, Speir JA et al. J Virol. 2012 Nov;86(21):11686-97.

Multimodal microtubule binding by the Ndc80 kinetochore complex. Alushin GM, Musinipally V et al. Nat Struct Mol Biol. 2012 Nov;19(11):1161-7.

Molecular architecture of human polycomb repressive complex 2. Ciferri C, Lander GC et al. eLife. 2012 Oct 30;1:e00005.

Multimolecule test-tube simulations of protein unfolding and aggregation. McCully ME, Beck DA, Daggett V. Proc Natl Acad Sci USA. 2012 Oct 30;109(44):17851-6.

Fiber diffraction data indicate a hollow core for the Alzheimer's aβ 3-fold symmetric fibril. McDonald M, Box H et al. J Mol Biol. 2012 Oct 26;423(3):454-61.

ATP-driven remodeling of the linker domain in the dynein motor. Roberts AJ, Malkova B et al. Structure. 2012 Oct 10;20(10):1670-80.

Neuromodulation by extracellular ATP and P2X receptors in the CNS. Khakh BS, North RA. Neuron. 2012 Oct 4;76(1):51-69.

Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane. Arolas JL, Broder C et al. Proc Natl Acad Sci USA. 2012 Oct 2;109(40):16131-6.

Computer-aided antibody design. Kuroda D, Shirai H et al. Protein Eng Des Sel. 2012 Oct;25(10):507-22.

Structural insights into catalysis by βC-S lyase from Streptococcus anginosus. Kezuka Y, Yoshida Y, Nonaka T. Proteins. 2012 Oct;80(10):2447-58.

Parallel molecular evolution in an herbivore community. Zhen Y, Aardema ML et al. Science. 2012 Sep 28;337(6102):1634-7.

Cross-neutralization of influenza A viruses mediated by a single antibody loop. Ekiert DC, Kashyap AK et al. Nature. 2012 Sep 27;489(7417):526-32.

Structural basis for microtubule binding and release by dynein. Redwine WB, Hernández-López R et al. Science. 2012 Sep 21;337(6101):1532-6.

Mutational analysis of residues involved in nucleotide and divalent cation stabilization in the rotavirus RNA-dependent RNA polymerase catalytic pocket. Ogden KM, Ramanathan HN, Patton JT. Virology. 2012 Sep 15;431(1-2):12-20.

Highly conserved protective epitopes on influenza B viruses. Dreyfus C, Laursen NS et al. Science. 2012 Sep 14;337(6100):1343-8.

Near-atomic resolution structural model of the yeast 26S proteasome. Beck F, Unverdorben P et al. Proc Natl Acad Sci USA. 2012 Sep 11;109(37):14870-5.

UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Yang Z, Lasker K et al. J Struct Biol. 2012 Sep;179(3):269-78.

Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Pintilie G, Chiu W. Biopolymers. 2012 Sep;97(9):742-60.

Room-temperature ferroelectricity in supramolecular networks of charge-transfer complexes. Tayi AS, Shveyd AK et al. Nature. 2012 Aug 23;488(7412):485-9.

Cartwheel architecture of Trichonympha basal body. Guichard P, Desfosses A et al. Science. 2012 Aug 3;337(6094):553.

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Pugh TJ, Weeraratne SD et al. Nature. 2012 Aug 2;488(7409):106-10.

The ERBB network: at last, cancer therapy meets systems biology. Yarden Y, Pines G. Nat Rev Cancer. 2012 Aug;12(8):553-63.

SALIGN: A web server for alignment of multiple protein sequences and structures. Braberg H, Webb BM et al. Bioinformatics. 2012 Aug 1;28(15):2072-3.

Interactions with DNA: Into the minor groove. Neidle S. Nat Chem. 2012 Aug;4(8):594-5.

Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy. Bharat TA, Davey NE et al. Nature. 2012 Jul 19;487(7407):385-9.

Molecular architecture and assembly principles of Vibrio cholerae biofilms. Berk V, Fong JC et al. Science. 2012 Jul 13;337(6091):236-9.

Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. Tran EE, Borgnia MJ et al. PLoS Pathog. 2012 Jul 12;8(7):e1002797.

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. Bakan A, Nevins N et al. J Chem Theory Comput. 2012 Jul 10;8(7):2435-2447.

Expanding molecular modeling and design tools to non-natural sidechains. Gfeller D, Michielin O, Zoete V. J Comput Chem. 2012 Jul 5;33(18):1525-35.

A Bayesian adaptive basis algorithm for single particle reconstruction. Kucukelbir A, Sigworth FJ, Tagare HD. J Struct Biol. 2012 Jul;179(1):56-67.

Genomics-aided structure prediction. Suƚkowska JI, Morcos F et al. Proc Natl Acad Sci USA. 2012 Jun 26;109(26):10340-5.

A movie of RNA polymerase II transcription. Cheung ACM, Cramer P. Cell. 2012 Jun 22;149(7):1431-7.

The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions. Faini M, Prinz S et al. Science. 2012 Jun 15;336(6087):1451-4.

An amino acid packing code for α-helical structure and protein design. Joo H, Chavan AG et al. J Mol Biol. 2012 Jun 8;419(3-4):234-54.

Molecular architecture of chemoreceptor arrays revealed by cryoelectron tomography of Escherichia coli minicells. Liu J, Hu B et al. Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):E1481-8.

Relevance of capsid structure in the buckling and maturation of spherical viruses. Aznar M, Luque A, Reguera D. Phys Biol. 2012 Jun;9(3):036003.

Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus T=3 capsid protein leads to larger T=4 capsids. Luque D, González JM et al. J Virol. 2012 Jun;86(12):6470-80.

Structure and size determination of bacteriophage P2 and P4 procapsids: Function of size responsiveness mutations. Dearborn AD, Laurinmaki P et al. J Struct Biol. 2012 Jun;178(3):215-24.

The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Ramrath DJ, Yamamoto H et al. Nature. 2012 May 24;485(7399):526-9.

Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen. Hu L, Crawford SE et al. Nature. 2012 May 10;485(7397):256-9.

Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. Greber BJ, Boehringer D et al. J Mol Biol. 2012 May 4;418(3-4):145-60.

Structural characterization of closely related O-antigen lipopolysaccharide (LPS) chain length regulators. Kalynych S, Yao D et al. J Biol Chem. 2012 May 4;287(19):15696-705.

Structure and dynamics of calmodulin (CaM) bound to nitric oxide synthase peptides: Effects of a phosphomimetic CaM mutation. Piazza M, Futrega K et al. Biochemistry. 2012 May 1;51(17):3651-61.

The cryo-EM structure of the UPF-EJC complex shows UPF1 poised toward the RNA 3' end. Melero R, Buchwald G et al. Nat Struct Mol Biol. 2012 May;19(5):498-505.

Cryo-EM structure of a transcribing cypovirus. Yang C, Ji G et al. Proc Natl Acad Sci USA. 2012 Apr 17;109(16):6118-23.

EBs recognize a nucleotide-dependent structural cap at growing microtubule ends. Maurer SP, Fourniol FJ et al. Cell. 2012 Apr 13;149(2):371-82.

Structural insights into initial and intermediate steps of the ribosome-recycling process. Yokoyama T, Shaikh TR et al. EMBO J. 2012 Apr 4;31(7):1836-46.

Fabs enable single particle cryoEM studies of small proteins. Wu S, Avila-Sakar A et al. Structure. 2012 Apr 4;20(4):582-92.

The molecular architecture of human Dicer. Lau PW, Guiley KZ et al. Nat Struct Mol Biol. 2012 Apr;19(4):436-40.

Topological analysis and interactive visualization of biological networks and protein structures. Doncheva NT, Assenov Y et al. Nat Protoc. 2012 Apr;7(4):670-85.

Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein. Zhang L, Yan F et al. Nat Chem Biol. 2012 Apr;8(4):342-9.

A structural model for the generation of continuous curvature on the surface of a retroviral capsid. Bailey GD, Hyun JK et al. J Mol Biol. 2012 Mar 30;417(3):212-23.

Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes. Feldman CR, Brodie ED Jr et al. Proc Natl Acad Sci USA. 2012 Mar 20;109(12):4556-61.

Allosteric antibody inhibition of human hepsin protease. Koschubs T, Dengl S et al. Biochem J. 2012 Mar 15;442(3):483-94.

Type VI secretion requires a dynamic contractile phage tail-like structure. Basler M, Pilhofer M et al. Nature. 2012 Mar 8;483(7388):182-6.

Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking. Baker MR, Rees I et al. Structure. 2012 Mar 7;20(3):450-63.

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Raychaudhuri S, Sandor C et al. Nat Genet. 2012 Mar;44(3):291-6.

Peripheral Ligand-binding Site in Cytochrome P450 3A4 Located with Fluorescence Resonance Energy Transfer (FRET). Davydov DR, Rumfeldt JA et al. J Biol Chem. 2012 Feb 24;287(9):6797-809.

Structure-function mapping of a heptameric module in the nuclear pore complex. Fernandez-Martinez J, Phillips J et al. J Cell Biol. 2012 Feb 20;196(4):419-34.

Complete subunit architecture of the proteasome regulatory particle. Lander GC, Estrin E et al. Nature. 2012 Feb 9;482(7384):186-91.

Subunit architecture of general transcription factor TFIIH. Gibbons BJ, Brignole EJ et al. Proc Natl Acad Sci USA. 2012 Feb 7;109(6):1949-54.

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography. Li S, Fernandez JJ et al. EMBO J. 2012 Feb 1;31(3):552-62.

Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle. Cong Y, Schröder GF et al. EMBO J. 2012 Feb 1;31(3):720-30.

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Raychaudhuri S, Sandor C et al. Nat Genet. 2012 Jan 29;44(3):291-6.

Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ. Malet H, Canellas F et al. Nat Struct Mol Biol. 2012 Jan 15;19(2):152-7.

Novel mycobacteria antigen 85 complex binding motif on fibronectin. Kuo CJ, Bell H et al. J Biol Chem. 2012 Jan 13;287(3):1892-902.

Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase. Lau WC, Rubinstein JL. Nature. 2012 Jan 12;481(7380):214-8.

The organisation of Ebola virus reveals a capacity for extensive, modular polyploidy. Beniac DR, Melito PL et al. PLoS One. 2012 Jan 11;7(1):e29608.

Crystal structure of Apis mellifera OBP14, a C-minus odorant-binding protein, and its complexes with odorant molecules. Spinelli S, Lagarde A et al. Insect Biochem Mol Biol. 2012 Jan;42(1):41-50.

The DARC site: a database of aligned ribosomal complexes. Jarasch A, Dziuk P et al. Nucleic Acids Res. 2012 Jan;40(1):D495-500.

How a DNA polymerase clamp loader opens a sliding clamp. Kelch BA, Makino DL et al. Science. 2011 Dec 23;334(6063):1675-80.

Remodeling of actin filaments by ADF/cofilin proteins. Galkin VE, Orlova A et al. Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20568-72.

The mechanism of DNA ejection in the Bacillus anthracis spore-binding phage 8a revealed by cryo-electron tomography. Fu X, Walter MH et al. Virology. 2011 Dec 20;421(2):141-8.

Structural conservation of the myoviridae phage tail sheath protein fold. Aksyuk AA, Kurochkina LP et al. Structure. 2011 Dec 7;19(12):1885-94.

Rhodopsin-transducin heteropentamer: Three-dimensional structure and biochemical characterization. Jastrzebska B, Ringler P et al. J Struct Biol. 2011 Dec;176(3):387-94.

A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield. Pejchal R, Doores KJ et al. Science. 2011 Nov 25;334(6059):1097-103.

Analysis of the interaction of the Eg5 Loop5 with the nucleotide site. Harrington TD, Naber N et al. J Theor Biol. 2011 Nov 21;289:107-15.

A mechanism for the evolution of phosphorylation sites. Pearlman SM, Serber Z, Ferrell JE Jr. Cell. 2011 Nov 11;147(4):934-46.

Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes. Chittuluru JR, Chaban Y et al. Nat Struct Mol Biol. 2011 Nov;18(11):1196–1203.

The evolution of function in strictosidine synthase-like proteins. Hicks MA, Barber AE 2nd et al. Proteins. 2011 Nov;79(11):3082-98.

Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor. Jomaa A, Stewart G et al. RNA. 2011 Nov;17(11):2026-38.

Characterization of PDZ domain-peptide interaction interface based on energetic patterns. Li N, Hou T et al. Proteins. 2011 Nov;79(11):3208-20.

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Umbarger MA, Toro E et al. Mol Cell. 2011 Oct 21;44(2):252-64.

Cryo-electron tomography reveals conserved features of doublet microtubules in flagella. Nicastro D, Fu X et al. Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):E845-53.

Progress in super long loop prediction. Zhao S, Zhu K et al. Proteins. 2011 Oct;79(10):2920-35.

The Staphylococcus aureus pathogenicity island 1 protein gp6 functions as an internal scaffold during capsid size determination. Dearborn AD, Spilman MS et al. J Mol Biol. 2011 Sep 30;412(4):710-22.

A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. Chappie JS, Mears JA et al. Cell. 2011 Sep 30;147(1):209-22.

Structures of the RNA-guided surveillance complex from a bacterial immune system. Wiedenheft B, Lander GC et al. Nature. 2011 Sep 21;477(7365):486-9.

Ligand discovery from a dopamine D(3) receptor homology model and crystal structure. Carlsson J, Coleman RG et al. Nat Chem Biol. 2011 Sep 18;7(11):769-78.

Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. Cavanaugh NA, Beard WA et al. J Biol Chem. 2011 Sep 9;286(36):31650-60.

The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. Allen GS, Wu CC et al. Structure. 2011 Sep 7;19(9):1219-32.

How does registry change of dynein's coiled-coil stalk drive binding of dynein to microtubule? Choi J, Park H, Seok C. Biochemistry. 2011 Sep 6;50(35):7629-36.

Brownian dynamics study of the association between the 70S ribosome and elongation factor G. Dƚugosz M, Huber GA et al. Biopolymers. 2011 Sep;95(9):616-27.

Visualization of bacteriophage P1 infection by cryo-electron tomography of tiny Escherichia coli. Liu J, Chen CY et al. Virology. 2011 Sep 1;417(2):304-11.