Volume 58; Issue 2

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Proteins: Structure, Function, and Bioinformatics
Volume 58; Issue 2

Proteins: Structure, Function, and Bioinformatics

Volume 58; Issue 2

1

Rational discovery of a novel interface for a coactivator in the peroxisome proliferator-activated receptor γ: Theoretical implications of impairment in type 2 diabetes mellitus

Takuma Shiraki, Takashi S. Kodama, Hisato Jingami, Narutoshi Kamiya

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 455 KB

english, 2005

2

Characterization of the denaturation of human α-lactalbumin in urea by molecular dynamics simulations

Lorna J. Smith, Rachel M. Jones, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.05 MB

english, 2005

3

MOLE: A data management application based on a protein production data model

Chris Morris, Peter Wood, Susanne L. Griffiths, Keith S. Wilson, Alun W. Ashton

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 240 KB

english, 2005

4

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein–DNA interface

Monika Radlinska, Aneta Kondrzycka-Dada, Andrzej Piekarowicz, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 476 KB

english, 2005

5

A generalized affine gap model significantly improves protein sequence alignment accuracy

Marcus A. Zachariah, Gavin E. Crooks, Stephen R. Holbrook, Steven E. Brenner

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 784 KB

english, 2005

6

Design of a data model for developing laboratory information management and analysis systems for protein production

Anne Pajon, John Ionides, Jon Diprose, Joël Fillon, Rasmus Fogh, Alun W. Ashton, Helen Berman, Wayne Boucher, Miroslaw Cygler, Emeline Deleury, Robert Esnouf, Joël Janin, Rosalind Kim, Isabelle Krimm,

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 677 KB

english, 2005

7

A molecular dynamics study of the structural stability of HIV-1 protease under physiological conditions: The role of Na+ ions in stabilizing the active site

Dmytro Kovalskyy, Volodymyr Dubyna, Alan E. Mark, Alexander Kornelyuk

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 958 KB

english, 2005

8

Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments

Hongyi Zhou, Yaoqi Zhou

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 95 KB

english, 2005

9

Extent of protein–protein interactions and quasi-equivalence in viral capsids

Craig M. Shepherd, Vijay S. Reddy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 230 KB

english, 2005

10

Quaternary structure is critical for protein display on capsid-like particles (CLPs): Efficient generation of hepatitis B virus CLPs presenting monomeric but not dimeric and tetrameric fluorescent proteins

Maren Vogel, Jolanta Vorreiter, Michael Nassal

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 841 KB

english, 2005

11

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics

Giacomo M.S. De Mori, Giorgio Colombo, Cristian Micheletti

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 514 KB

english, 2005

12

Structural evidence for variable oligomerization of the N-terminal domain of cyclase-associated protein (CAP)

Adlina Mohd Yusof, Nien-Jen Hu, Alexander Wlodawer, Andreas Hofmann

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 719 KB

english, 2005

13

Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region

Yosuke Tajika, Naoki Sakai, Tomohiro Tamura, Min Yao, Nobuhisa Watanabe, Isao Tanaka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 487 KB

english, 2005

14

Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae

Debanu Das, Natasha Oganesyan, Hisao Yokota, Ramona Pufan, Rosalind Kim, Sung-Hou Kim

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 338 KB

english, 2005

15

Crystal structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8

Nobutaka Numoto, Akiko Kita, Kunio Miki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 109 KB

english, 2005

16

Issues in high-throughput comparative modelling: A case study using the ubiquitin E2 conjugating enzymes

P.J. Winn, J.N.D. Battey, K. Schleinkofer, A. Banerjee, R.C. Wade

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 313 KB

english, 2005

17

Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways

N. Rekha, S.M. Machado, C. Narayanan, A. Krupa, N. Srinivasan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 864 KB

english, 2005

18

Structure and dynamics of the human pleckstrin DEP domain: Distinct molecular features of a novel DEP domain subfamily

Concepcion Civera, Bernd Simon, Gunter Stier, Michael Sattler, Maria J. Macias

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.16 MB

english, 2005

19

Predicting protein functional sites with phylogenetic motifs

David La, Brian Sutch, Dennis R. Livesay

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 452 KB

english, 2005

20

The solution structure of BmTx3B, a member of the scorpion toxin subfamily α-KTx 16

Yuefeng Wang, Xiang Chen, Naixia Zhang, Gong Wu, Houming Wu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 351 KB

english, 2005

21

Topological determinants of protein unfolding rates

Jaewoon Jung, Jooyoung Lee, Hie-Tae Moon

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 320 KB

english, 2005

22

PhosphaBase: An ontology-driven database resource for protein phosphatases

K. J. Wolstencroft, R. Stevens, L. Tabernero, A. Brass

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 135 KB

english, 2005

23

Receptor rigidity and ligand mobility in trypsin–ligand complexes

Olgun Guvench, Daniel J. Price, Charles L. Brooks III

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 353 KB

english, 2005

24

Analysis of pH-dependent elements in proteins: Geometry and properties of pairs of hydrogen-bonded carboxylic acid side-chains

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 379 KB

english, 2005

25

Structural classification of thioredoxin-like fold proteins

Yuan Qi, Nick V. Grishin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 2.04 MB

english, 2005

26

Elucidation of information encoded in tryptophan 140 of staphylococcal nuclease

Satoshi Hirano, Hironari Kamikubo, Yoichi Yamazaki, Mikio Kataoka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 285 KB

english, 2005

27

Theoretical investigations of prostatic acid phosphatase

Satyan Sharma, Päivi Pirilä, Helena Kaija, Katja Porvari, Pirkko Vihko, André H. Juffer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 552 KB

english, 2005

28

Effect of T-R conformational change on sickle-cell hemoglobin interactions and aggregation

S. M. Vaiana, M. A. Rotter, A. Emanuele, F. A. Ferrone, M. B. Palma-Vittorelli

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 367 KB

english, 2005