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Citations (partial list)

Structural insights into RNA processing by the human RISC-loading complex. Wang HW, Noland C et.al. Nat Struct Mol Biol. 2009 Nov;16(11):1148-53.

Accuracy analysis of multiple structure alignments. Berbalk C, Schwaiger CS, Lackner P. Protein Sci. 2009 Oct;18(10):2027-35.

10-Å cryoEM structure and molecular model of the Myriapod (Scutigera) 6x6mer hemocyanin: understanding a giant oxygen transport protein. Markl J, Moeller A et.al. J Mol Biol. 2009 Sep 18;392(2):362-80.

Structural changes to monomeric CuZn superoxide dismutase caused by the familial amyotrophic lateral sclerosis-associated mutation A4V. Schmidlin T, Kennedy BK, Daggett V. Biophys J. 2009 Sep 16;97(6):1709-18.

A dimeric structure for archaeal box C/D small ribonucleoproteins. Bleichert F, Gagnon KT et.al. Science. 2009 Sep 11;325(5946):1384-7.

Structure of the BK potassium channel in a lipid membrane from electron cryomicroscopy. Wang L, Sigworth FJ. Nature. 2009 Sep 10;461(7261):292-5.

Through-Space Effects of Substituents Dominate Molecular Electrostatic Potentials of Substituted Arenes. SE Wheeler, KN Houk. J Chem Theory Comput. 2009 Sep 8;5(9):2301-12.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning. Danziger SA, Baronio R et.al. PLoS Comput Biol. 2009 Sep;5(9):e1000498.

GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics. Allen WJ, Lemkul JA, Bevan DR. J Comput Chem. 2009 Sep;30(12):1952-8.

Allosteric modulation of DNA by small molecules. Chenoweth DM, Dervan PB. Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13175-9.

Escherichia coli DegP: a structure-driven functional model. Ortega J, Iwanczyk J, Jomaa A J Bacteriol. 2009 Aug;191(15):4705-13.

Paramyxovirus ultrastructure and genome packaging: cryo-electron tomography of sendai virus. Loney C, Mottet-Osman G et.al. J Virol. 2009 Aug;83(16):8191-7.

An icosahedral algal virus has a complex unique vertex decorated by a spike. Cherrier MV, Kostyuchenko VA et.al. Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11085-9.

Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Kampmann M, Blobel G Nat Struct Mol Biol. 2009 Jul;16(7):782-8.

IMP dehydrogenase: structure, mechanism, and inhibition. Hedstrom L Chem Rev. 2009 Jul;109(7):2903-28.

A generalized knowledge-based discriminatory function for biomolecular interactions. Bernard B, Samudrala R Proteins. 2009 Jul;76(1):115-128.

Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the Beta-Lactamase Inhibitory Proteins BLIP, BLIP-I and BLP. Gretes M, Lim DC et.al. J Mol Biol. 2009 Jun 5;389(2):289-305.

DOCK 6: Combining techniques to model RNA-small molecule complexes. Lang PT, Brozell SR et.al. RNA. 2009 Jun;15(6):1219-30.

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Ryan M, Diekhans M et.al. Bioinformatics. 2009 Jun 1;25(11):1431-2.

Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Xiang Y, Leiman PG et.al. Mol Cell. 2009 May 15;34(3):375-86.

Mass spectrometry-based structural dissection of fluorescent proteins. Alvarez LA, Merola F et.al. Biochemistry. 2009 May 12;48(18):3810-2.

Structure-function relationships of the outer membrane translocon Wza investigated by cryo-electron microscopy and mutagenesis. Ford RC, Brunkan-LaMontagne AL et.al. J Struct Biol. 2009 May;166(2):172-82.

Structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group. Verma SK, Jaiswal M et.al. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 May 1;65(Pt 5):435-9.

Structure of rat odorant-binding protein OBP1 at 1.6 A resolution. White SA, Briand L et.al. Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):403-10.

DNA binding site sequence directs glucocorticoid receptor structure and activity. Meijsing SH, Pufall MA et.al. Science. 2009 Apr 17;324(5925):407-10.

Coordinated movement of cytoplasmic and transmembrane domains of RyR1 upon gating. Samsó M, Feng W et.al. PLoS Biology. 2009 Apr 14;7(4):e85.

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. Pieper U, Chiang R et.al. J Struct Funct Genomics. 2009 Apr;10(2):107-125.

Characterization of cell-surface prion protein relative to its recombinant analogue: insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. DeMarco ML, Daggett V J Neurochem. 2009 Apr;109(1):60-73.

Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface. Kuroda D, Shirai H et.al. Proteins. 2009 Apr;75(1):139-46.

Heparin binding induces conformational changes in Adeno-associated virus serotype 2. Levy HC, Bowman VD et.al. J Struct Biol. 2009 Mar;165(3):146-56.

Visualization of a missing link in retrovirus capsid assembly. Cardone G, Purdy JG et.al. Nature. 2009 Feb 5;457(7230):694-8.

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH et.al. PLoS ONE. 2009 Feb 3;4(2):e4345.

Conformational flexibility of metazoan fatty acid synthase enables catalysis. Brignole EJ, Smith S, Asturias FJ Nat Struct Mol Biol. 2009 Feb;16(2):190-7.

Predicting druggable binding sites at the protein-protein interface. Fuller JC, Burgoyne NJ, Jackson RM Drug Discov Today. 2009 Feb;14(3-4):155-61.

Rotavirus architecture at subnanometer resolution. Li Z, Baker ML et.al. J Virol. 2009 Feb;83(4):1754-66.

Boer DR, Canals A, Coll M DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans. 2009 Jan 21;(3):399-414.

Ghosh D, Griswold J et.al. Structural basis for androgen specificity and oestrogen synthesis in human aromatase. Nature. 2009 Jan 8;457(7226):219-23.

Sharma J, Chhabra R et.al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science. 2009 Jan 2;323(5910):112-6.

Vonck J, Schäfer E Supramolecular organization of protein complexes in the mitochondrial inner membrane. Biochim Biophys Acta. 2009 Jan;1793(1):117-24.

Pieper U, Eswar N et.al. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan;37:D347-D354.

Abeln S, Frenkel D Disordered flanks prevent peptide aggregation. PLoS Comput Biol. 2008 Dec;4(12):e1000241.

Julián P, Konevega AL et.al. Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc Natl Acad Sci USA. 2008 Nov 4;105(44):16924-7.

Freiberg AN, Sherman MB et.al. Three-dimensional organization of Rift Valley fever virus revealed by cryoelectron tomography. J Virol. 2008 Nov;82(21):10341-8.

Johnson CH, Egli M, Stewart PL Structural insights into a circadian oscillator. Science. 2008 Oct 31;322(5902):697-701.

Burkowski FJ Structural Bioinformatics: An Algorithmic Approach. Series: Chapman & Hall/CRC Mathematical & Computational Biology. Publication Date: 10/30/2008.

Shafrir Y, Durell SR, Guy HR Models of the structure and gating mechanisms of the pore domain of the NaChBac ion channel. Biophys J. 2008 Oct;95(8):3650-62.

Khursigara CM, Wu X, Subramaniam S Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed array. J Bacteriol. 2008 Oct;190(20):6805-10.

Miller PS, Topf M, Smart TG Mapping a molecular link between allosteric inhibition and activation of the glycine receptor. Nat Struct Mol Biol. 2008 Oct;15(10):1084-93.

Jones S, Zhang X et.al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26;321(5897):1801-6.

Parsons DW, Jones S et.al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26;321(5897):1807-12.

Liu J, Bartesaghi A et.al. Molecular architecture of native HIV-1 gp120 trimers. Nature. 2008 Sep 4;455(7209):109-13.

Min D, Josephine HR et.al. An enzymatic atavist revealed in dual pathways for water activation. PLoS Biol. 2008 Aug 26;6(8):e206.

Jiang J, Zhang X et.al. Activation of DegP chaperone-protease via formation of large cage-like oligomers upon binding to substrate proteins. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11939-44.

Sellers BD, Zhu K et.al. Toward better refinement of comparative models: predicting loops in inexact environments. Proteins. 2008 Aug 15;72(3):959-71.

Koglin A, Löhr F et.al. Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature. 2008 Aug 14;454(7206):907-11.

Lawson CL, Dutta S et.al. Representation of viruses in the remediated PDB archive. Acta Crystallogr D Biol Crystallogr. 2008 Aug;64(Pt 8):874-82.

Fromer M, Yanover C A computational framework to empower probabilistic protein design. Bioinformatics. 2008 Jul 1;24(13):i214-22.

Ménétret JF, Hegde RS et.al. Single copies of Sec61 and TRAP associate with a nontranslating mammalian ribosome. Structure. 2008 Jul;16(7):1126-37.

Dietrich KA, Sindelar CV et.al. The kinesin-1 motor protein is regulated by a direct interaction of its head and tail. Proc Natl Acad Sci USA. 2008 Jul 1;105(26):8938-43.

Joubès J, Raffaele S et.al. The VLCFA elongase gene family in Arabidopsis thaliana: phylogenetic analysis, 3D modelling and expression profiling. Plant Mol Biol. 2008 Jul;67(5):547-66.

Pattanayek R, Williams DR et.al. Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation. EMBO J. 2008 Jun 18;27(12):1767-78.

Auer M, Koster AJ et.al. Three-dimensional Architecture of Hair-bundle Linkages Revealed by Electron-microscopic Tomography. J Assoc Res Otolaryngol. 2008 Jun;9(2):215-24.

Beck DA, Jonsson AL et.al. Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations. Protein Eng Des Sel. 2008 Jun;21(6):353-68.

Banerjee R, Gretes M et.al. In vitro selection and characterization of ceftobiprole-resistant methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 2008 Jun;52(6):2089-96.

Lambert AR, Sussman D et.al. Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding. Structure. 2008 Apr 8;16(4):558-69.

Scott KA, Bond PJ et.al. Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly. Structure. 2008 Apr 8;16(4):621-630.

McErlean P, Shackelton LA et.al. Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS ONE. 2008 Apr 2;3(4):e1847.

He Y, Ye T et.al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature. 2008 Mar 13;452(7184):198-201.

Sagara T, Ganz E Calculations of Dihydrogen Binding to Doped Carbon Nanostructures. J Phys Chem C. 2008 Mar 13;112(10):3515-8.

Jiang W, Baker ML et.al. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature. 2008 Feb 28;451(7182):1130-4.

Fischer A, Garcia-Rodriguez C et.al. Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy. J Biol Chem. 2008 Feb 15;283(7):3997-4003.

Lee J, Seok C A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect. Proteins. 2008 Feb 15;70(3):1074-83.

Zhang X, Settembre E et.al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1867-72.

Merkley ED, Bernard B, Daggett V Conformational Changes below the T(m): Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A. Biochemistry. 2008 Jan 22;47(3):880-92.

Andrecka J, Lewis R et.al. Single-molecule tracking of mRNA exiting from RNA polymerase II. Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):135-40.

Sacchettini JC, Rubin EJ, Freundlich JS Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat Rev Microbiol. 2008 Jan;6(1):41-52.

Xiang Y, Goodman MF et.al. Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins. 2008 Jan 1;70(1):231-47.

Ménétret JF, Schaletzky J et.al. Ribosome binding of a single copy of the SecY complex: implications for protein translocation. Mol Cell. 2007 Dec 28;28(6):1083-92.

London N, Schueler-Furman O Assessing the energy landscape of CAPRI targets by FunHunt. Proteins. 2007 Dec 1;69(4):809-15.

Alber F, Dokudovskaya S et.al. The molecular architecture of the nuclear pore complex. Nature. 2007 Nov 29;450(7170):695-701.

Wood LD, Parsons DW et.al. The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16;318(5853):1108-13.

Abyzov A, Ilyin VA A comprehensive analysis of non-sequential alignments between all protein structures. BMC Struct Biol. 2007 Nov 16;7:78.

Beniac DR, Devarennes SL et.al. Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion. PLoS ONE. 2007 Oct 24;2(10):e1082.

Gherardini PF, Wass MN et.al. Convergent evolution of enzyme active sites is not a rare phenomenon. J Mol Biol. 2007 Sep 21;372(3):817-45.

Moad AJ, Moad CW et.al. NLOPredict: Visualization and data analysis software for nonlinear optics. J Comput Chem. 2007 Sep;28(12):1996-2002.

Chiu PL, Pagel MD et.al. The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution. Structure. 2007 Sep;15(9):1053-64.

Tolstorukov MY, Colasanti AV et.al. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol. 2007 Aug 17;371(3):725-38.

Leiman PG, Battisti AJ et.al. The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J Mol Biol. 2007 Aug 17;371(3):836-49.

Hu Y, Ren Y et.al. Novel mutations of the lipoprotein lipase gene associated with hypertriglyceridemia in members of type 2 diabetic pedigrees. J Lipid Res. 2007 Aug;48(8):1681-8.

Manuell AL, Quispe J, Mayfield SP Structure of the chloroplast ribosome: novel domains for translation regulation. PLoS Biol. 2007 Aug;5(8):e209.

Zoete V, Grosdidier A, Michielin O Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and interactions with regulators. Biochim Biophys Acta. 2007 Aug;1771(8):915-25.

Wang HW, Ramey VH et.al. Architecture of the Dam1 kinetochore ring complex and implications for microtubule-driven assembly and force-coupling mechanisms. Nat Struct Mol Biol. 2007 Aug;14(8):721-6.

Villoutreix BO, Renault N et.al. Free resources to assist structure-based virtual ligand screening experiments. Curr Protein Pept Sci. 2007 Aug;8(4):381-411.

Ojha S, Meng EC, Babbitt PC Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins. PLoS Comput Biol. 2007 Jul 20;3(7):e121

Morris JH, Huang CC et.al. structureViz: Linking Cytoscape and UCSF Chimera. Bioinformatics 2007 Jul 10; [Epub ahead of print]

Kelley LL, Dillard BD et.al. Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 A resolution. Acta Crystallograph Sect F Struct Biol Cryst Commun. 2007 Jul 1;63(Pt 7):549-52.

Tungtur S, Egan SM, Swint-Kruse L Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence. Proteins. 2007 Jul 1;68(1):375-88.

Quilis J, Meynard D et.al. A potato carboxypeptidase inhibitor gene provides pathogen resistance in transgenic rice. Plant Biotechnol J. 2007 Jul;5(4):537-53.

Torreira E, Schoehn G et.al. Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer. Nucleic Acids Res. 2007 Jun;35(11):3774-83.