Volume 65; Issue 3

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Proteins: Structure, Function, and Bioinformatics
Volume 65; Issue 3

Proteins: Structure, Function, and Bioinformatics

Volume 65; Issue 3

1

Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 Å resolution reveals a new fold with a novel active site

Michael DiDonato, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Sanjay Agarwalla, Scott M. Brittain, Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Herbert L. Axelrod, Jaume M. Canaves,

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.10 MB

english, 2006

2

Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 Å resolution reveals a fold similar to the Ran-binding protein Mog1p

Qingping Xu, S. Sri Krishna, Daniel McMullan, Robert Schwarzenbacher, Mitchell D. Miller, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Tamara Astakhova, Herbert L. Axelrod, Jaume M. Canaves, Dennis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 444 KB

english, 2006

3

Specificity of molecular interactions in transient protein–protein interaction interfaces

Kyu-il Cho, KiYoung Lee, Kwang H. Lee, Dongsup Kim, Doheon Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 625 KB

english, 2006

4

Characterization and tissue-specific expression of two lepidopteran farnesyl diphosphate synthase homologs: Implications for the biosynthesis of ethyl-substituted juvenile hormones

Michel Cusson, Catherine Béliveau, Stephanie E. Sen, Sophie Vandermoten, Robert G. Rutledge, Don Stewart, Frédéric Francis, Éric Haubruge, Peter Rehse, David J. Huggins, Ashley P.G. Dowling, Guy H. Gr

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 698 KB

english, 2006

5

Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design

Zhigang Zhou, Maria Bates, Jeffry D. Madura

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.53 MB

english, 2006

6

ROSETTALIGAND: Protein–small molecule docking with full side-chain flexibility

Jens Meiler, David Baker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 760 KB

english, 2006

7

Kinetic and structural properties of inorganic pyrophosphatase from the pathogenic bacterium Helicobacter pylori

Ti-Chun Chao, Haimei Huang, Jia-Yin Tsai, Chung-Yu Huang, Yuh-Ju Sun

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 580 KB

english, 2006

8

NMR structure of protein PA2021 from Pseudomonas aeruginosa

Yu-Chieh Lin, Gaohua Liu, Yang Shen, Claudia Bertonati, Adelinda Yee, Barry Honig, Cheryl H. Arrowsmith, Thomas Szyperski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 135 KB

english, 2006

9

Structural dynamics of the mitochondrial ADP/ATP carrier revealed by molecular dynamics simulation studies

M. Falconi, G. Chillemi, D. Di Marino, I. D'Annessa, B. Morozzo della Rocca, L. Palmieri, A. Desideri

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 723 KB

english, 2006

10

Docking of human interleukin-15 to its specific receptor α chain: Correlation between molecular modeling and mutagenesis experimental data

Agnès Quéméner, Jérôme Bernard, Erwan Mortier, Ariane Plet, Yannick Jacques, Vinh Tran

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 773 KB

english, 2006

11

Physicochemical descriptors to discriminate protein–protein interactions in permanent and transient complexes selected by means of machine learning algorithms

Peter Block, Juri Paern, Eyke Hüllermeier, Paul Sanschagrin, Christoph A. Sotriffer, Gerhard Klebe

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 463 KB

english, 2006

12

Crystal structure of the conserved hypothetical cytosolic protein Xcc0516 from Xanthomonas campestris reveals a novel quaternary structure assembled by five four-helix bundles

Li-Ying Lin, Chung-Lun Ching, Ko-Hsin Chin, Shan-Ho Chou, Nei-Li Chan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 277 KB

english, 2006

13

Computational and experimental approaches for assessing the interactions between the model calycin β-lactoglobulin and two antibacterial fluoroquinolones

Ivano Eberini, Piercarlo Fantucci, Alessandro Guerini Rocco, Elisabetta Gianazza, Lara Galluccio, Daniela Maggioni, Ilaria Dal Ben, Monica Galliano, Rosalba Mazzitello, Noura Gaiji, Tiziana Beringhell

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 562 KB

english, 2006

14

Structural basis for the observed differential magnetic anisotropic tensorial values in calcium binding proteins

Sourajit M. Mustafi, Sulakshana Mukherjee, Kandala V. R. Chary, Gabriele Cavallaro

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 784 KB

english, 2006

15

Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 695 KB

english, 2006

16

Stereochemistry of guanidine–metal interactions: Implications for L-arginine–metal interactions in protein structure and function

Luigi Di Costanzo, Lloyd V. Flores Jr., David W. Christianson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 453 KB

english, 2006

17

Homology modeling and molecular dynamics study of West Nile virus NS3 protease: A molecular basis for the catalytic activity increased by the NS2B cofactor

Hong Zhou, N. Jiten Singh, Kwang S. Kim

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 429 KB

english, 2006

18

Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 Å resolution

Mickey Kosloff, Gye Won Han, S. Sri Krishna, Robert Schwarzenbacher, Marc Fasnacht, Marc-André Elsliger, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Tamara Astakhova, Herbert L. Axelrod, Jaume M.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 970 KB

english, 2006

19

Prediction of EF-hand calcium-binding proteins and analysis of bacterial EF-hand proteins

Yubin Zhou, Wei Yang, Michael Kirberger, Hsiau-Wei Lee, Gayatri Ayalasomayajula, Jenny J. Yang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 583 KB

english, 2006

20

Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: Comparisons of the wild-type protein, a b-type variant, and the apo state

Lorna J. Smith, Robert J. Davies, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 417 KB

english, 2006

21

Thermal versus mechanical unfolding of ubiquitin

Anders Irbäck, Simon Mitternacht

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 342 KB

english, 2006

22

Generalized modeling of enzyme–ligand interactions using proteochemometrics and local protein substructures

Helena Strömbergsson, Andriy Kryshtafovych, Peteris Prusis, Krzysztof Fidelis, Jarl E. S. Wikberg, Jan Komorowski, Torgeir R. Hvidsten

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 527 KB

english, 2006

23

Critical assessment of the automated AutoDock as a new docking tool for virtual screening

Hwangseo Park, Jinuk Lee, Sangyoub Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 323 KB

english, 2006

24

A novel high resolution CαCα distance dependent force field based on a high quality decoy set

R. Rajgaria, S. R. McAllister, C. A. Floudas

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 491 KB

english, 2006

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