Volume 61; Issue 4

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Proteins: Structure, Function, and Bioinformatics
Volume 61; Issue 4

Proteins: Structure, Function, and Bioinformatics

Volume 61; Issue 4

1

Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study

G. Fiorin, R. R. Biekofsky, A. Pastore, P. Carloni

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 481 KB

english, 2005

2

Sensitive detection of sequence similarity using combinatorial pattern discovery: A challenging study of two distantly related protein families

Nikos Darzentas, Isidore Rigoutsos, Christos A. Ouzounis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.01 MB

english, 2005

3

Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 Å resolution reveals a new fold

Heath E. Klock, Robert Schwarzenbacher, Qingping Xu, Daniel McMullan, Polat Abdubek, Eileen Ambing, Herbert Axelrod, Tanya Biorac, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDonato, M

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 275 KB

english, 2005

4

Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets

Georg Fuellen, Michael Spitzer, Paul Cullen, Stefan Lorkowski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 507 KB

english, 2005

5

Functional restraints on the patterns of amino acid substitutions: Application to sequence–structure homology recognition

Vijayalakshmi Chelliah, Tom Blundell, Kenji Mizuguchi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 565 KB

english, 2005

6

Crystal structure of the hypothetical protein ST2072 from Sulfolobus tokodaii

Yoshikazu Tanaka, Kouhei Tsumoto, Eiki Tanabe, Yoshiaki Yasutake, Naoki Sakai, Min Yao, Isao Tanaka, Izumi Kumagai

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 329 KB

english, 2005

7

Compact reduced thioredoxin structure from the thermophilic bacteria Thermus thermophilus

Peter H. Rehse, Maki Kumei, Tahir H. Tahirov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 288 KB

english, 2005

8

Refinement of unbound protein docking studies using biological knowledge

Philipp Heuser, Davide Baù, Pascal Benkert, Dietmar Schomburg

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 145 KB

english, 2005

9

Multiple display of a protein domain on a bacterial polymeric scaffold

P. O. Craig, P. M. Berguer, N. Ainciart, V. Zylberman, M. G. Thomas, L. J. Martinez Tosar, A. Bulloj, G. L. Boccaccio, F. A. Goldbaum

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 492 KB

english, 2005

10

Solution structures of the reduced and Cu(I) bound forms of the first metal binding sequence of ATP7A associated with Menkes disease

Tara M. DeSilva, Gianluigi Veglia, Stanley J. Opella

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 433 KB

english, 2005

11

Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues

G. Archontis, K. A. Watson, Q. Xie, G. Andreou, E. D. Chrysina, S. E. Zographos, N. G. Oikonomakos, M. Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 522 KB

english, 2005

12

Crystal structure of a new class of glutathione transferase from the model human hookworm nematode Heligmosomoides polygyrus

David J. Schuller, Qun Liu, Irina A. Kriksunov, Alison M. Campbell, John Barrett, Peter M. Brophy, Quan Hao

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 943 KB

english, 2005

13

Focused library design in GPCR projects on the example of 5-HT2c agonists: Comparison of structure-based virtual screening with ligand-based search methods

Caterina Bissantz, Claire Schalon, Wolfgang Guba, Martin Stahl

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 919 KB

english, 2005

14

Knowledge-based voting algorithm for automated protein functional annotation

G.X. Yu, E.M. Glass, N.T. Karonis, N. Maltsev

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 404 KB

english, 2005

15

Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase

Kimberly A. Watson, Evangelia D. Chrysina, Katerina E. Tsitsanou, Spyros E. Zographos, Georgios Archontis, George W.J. Fleet, Nikos G. Oikonomakos

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 681 KB

english, 2005

16

Solution structure of HP1242 from Helicobacter pylori

Su-Jin Kang, Sung Jean Park, Seo-Jeong Jung, Bong-Jin Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 129 KB

english, 2005

17

Origin of the sequence-dependent polyproline II structure in unfolded peptides

Alex Kentsis, Mihaly Mezei, Roman Osman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 265 KB

english, 2005

18

External cross-validation for unbiased evaluation of protein family detectors: Application to allergens

Daniel Soeria-Atmadja, Mikael Wallman, Åsa K. Björklund, Anders Isaksson, Ulf Hammerling, Mats G. Gustafsson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 290 KB

english, 2005

19

Very fast empirical prediction and rationalization of protein pKa values

Hui Li, Andrew D. Robertson, Jan H. Jensen

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 422 KB

english, 2005

20

Structural characterization of proteins using residue environments

Sean D. Mooney, Mike Hsin-Ping Liang, Rob DeConde, Russ B. Altman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 636 KB

english, 2005

21

Use of bioinformatics tools for the annotation of disease-associated mutations in animal models

Carles Ferrer-Costa, Modesto Orozco, Xavier de la Cruz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 311 KB

english, 2005

22

Crystal structure of the small form of glucose-inhibited division protein A from Thermus thermophilus HB8

Wakana Iwasaki, Hideyuki Miyatake, Kunio Miki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 385 KB

english, 2005

23

Protein loop structure prediction with flexible stem geometries

M. Mönnigmann, C.A. Floudas

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 869 KB

english, 2005

24

A tetrapeptide-based method for polyproline II-type secondary structure prediction

Peter K. Vlasov, Anna V. Vlasova, Vladimir G. Tumanyan, Natalia G. Esipova

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 132 KB

english, 2005

25

Deuterium oxide promotes assembly and bundling of FtsZ protofilaments

Manas Kumar Santra, Debjani Dasgupta, Dulal Panda

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 395 KB

english, 2005

26

Comparative molecular dynamics—Similar folds and similar motions?

Andrew Pang, Yalini Arinaminpathy, Mark S. P. Sansom, Philip C. Biggin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.25 MB

english, 2005

27

Crystal structure of the putative RNA methyltransferase PH1948 from Pyrococcus horikoshii, in complex with the copurified S-adenosyl-L-homocysteine

Yong-Gui Gao, Min Yao, Zhou Yong, Isao Tanaka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 362 KB

english, 2005

28

Crystal structure of putative N-Acetyl-γ-glutamyl-phosphate reductase (AK071544) from rice (Oryza sativa)

Tsuyoshi Nonaka, Akiko Kita, Jun Miura-Ohnuma, Etsuko Katoh, Noritoshi Inagaki, Toshimasa Yamazaki, Kunio Miki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 261 KB

english, 2005

29

An intuitive approach to measuring protein surface curvature

Ryan G. Coleman, Michael A. Burr, Diane L. Souvaine, Alan C. Cheng

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 247 KB

english, 2005

30

The impact of the fourth disulfide bridge in scorpion toxins of the α-KTx6 subfamily

Louis Carrega, Amor Mosbah, Gilles Ferrat, Christine Beeton, Nicolas Andreotti, Pascal Mansuelle, Hervé Darbon, Michel De Waard, Jean-Marc Sabatier

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 685 KB

english, 2005

31

Effects of environment on the structure of Pyrococcus furiosus rubredoxin: A molecular dynamics study

Can E. Ergenekan, Ming-Liang Tan, Toshiko Ichiye

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 259 KB

english, 2005

32

Mutagenesis at Pro309 of single-chain urokinase-type plasminogen activator alters its catalytic properties

Ziyong Sun, Jian-Ning Liu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 109 KB

english, 2005

33

Rational genomics I: Antisense open reading frames and codon bias in short-chain oxido reductase enzymes and the evolution of the genetic code

William L. Duax, Robert Huether, Vladimir Z. Pletnev, David Langs, Anthony Addlagatta, Sonjay Connare, Lukas Habegger, Jay Gill

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 297 KB

english, 2005

34

Molecular docking of balanol to dynamics snapshots of protein kinase A

Chung F. Wong, Jeremy Kua, Yingkai Zhang, T.P. Straatsma, J. Andrew McCammon

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 299 KB

english, 2005

35

Folding behavior of chaperonin-mediated substrate protein

Wei-Xin Xu, Jun Wang, Wei Wang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 731 KB

english, 2005

36

Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

Suwipa Saen-oon, Mayuso Kuno, Supa Hannongbua

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 603 KB

english, 2005

37

Solution structure of conserved hypothetical protein HP0894 from Helicobacter pylori

Kyung-Doo Han, Sung-Jean Park, Sun-Bok Jang, Woo-Sung Son, Bong-Jin Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 146 KB

english, 2005

38

Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8

Motoyuki Hattori, Eiichi Mizohata, Miho Manzoku, Yoshitaka Bessho, Kazutaka Murayama, Takaho Terada, Seiki Kuramitsu, Mikako Shirouzu, Shigeyuki Yokoyama

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 482 KB

english, 2005

39

Survey of the geometric association of domain–domain interfaces

Wan Kyu Kim, Jon C. Ison

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 624 KB

english, 2005

40

Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data

Husheng Ding, Yuedong Yang, Jiahai Zhang, Jihui Wu, Haiyan Liu, Yunyu Shi

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 307 KB

english, 2005

41

Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study

Phuong H. Nguyen, Gerhard Stock, Emil Mittag, Chin-Kun Hu, Mai Suan Li

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.21 MB

english, 2005

42

Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

Pierre Tuffery, Philippe Derreumaux

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 284 KB

english, 2005

43

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8

Ihsanawati, Takashi Kumasaka, Tomonori Kaneko, Chihiro Morokuma, Rie Yatsunami, Takao Sato, Satoshi Nakamura, Nobuo Tanaka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.27 MB

english, 2005

44

Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin

Jongkeun Choi, Soonwoong Choi, Jae Kyung Chon, Jungwon Choi, Mee-Kyung Cha, Il-Han Kim, Whanchul Shin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 256 KB

english, 2005

45

Weighing in on a timeless controversy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 198 KB

english, 2005

46

Electrostatic potential at the retinal of three archaeal rhodopsins: Implications for their different absorption spectra

Edda Kloppmann, Torsten Becker, G. Matthias Ullmann

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 366 KB

english, 2005

47

Structural differences between allelic variants of the ovine prion protein revealed by molecular dynamics simulations

Raymond Bujdoso, David F. Burke, Alana M. Thackray

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.08 MB

english, 2005

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