Volume 63; Issue 4

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Proteins: Structure, Function, and Bioinformatics
Volume 63; Issue 4

Proteins: Structure, Function, and Bioinformatics

Volume 63; Issue 4

1

Crystal structure of hypothetical protein YfiH from Shigella flexneri at 2 Å resolution

Youngchang Kim, Natalia Maltseva, Irina Dementieva, Frank Collart, Denise Holzle, Andrzej Joachimiak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 247 KB

english, 2006

2

Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution

Irimpan I. Mathews, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Polat Abdubek, Eileen Ambing, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDonato, Marc-André Elsliger, Adam

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.47 MB

english, 2006

3

1.6 Å Crystal structure of a PA2721 protein from pseudomonas aeruginosa—A potential drug-resistance protein

B. Nocek, M. Cuff, E. Evdokimova, A. Edwards, A. Joachimiak, A. Savchenko

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 208 KB

english, 2006

4

Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors

Jinfeng Zhang, Rong Chen, Jie Liang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 279 KB

english, 2006

5

Structural characterization of an iron–sulfur cluster assembly protein IscU in a zinc-bound form

Jinyu Liu, Natalia Oganesyan, Dong-Hae Shin, Jarmila Jancarik, Hisao Yokota, Rosalind Kim, Sung-Hou Kim

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 31 KB

english, 2006

6

Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

Francisco Melo, Marc A. Marti-Renom

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 205 KB

english, 2006

7

Structures of intact glycoproteins from vibrational circular dichroism

Ganesh Shanmugam, Prasad L. Polavarapu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 341 KB

english, 2006

8

Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses

Catherine H. Schein, David E. Volk, Numan Oezguen, Aniko Paul

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 301 KB

english, 2006

9

Crystal structure of TM1367 from Thermotoga maritima at 1.90 Å resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Kevin Kai Jin, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Herbert Axelrod, Jaume M. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Michael DiDon

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 848 KB

english, 2006

10

On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites

Murad Nayal, Barry Honig

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 570 KB

english, 2006

11

A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors

Kai Ye, Eric-Wubbo M. Lameijer, Margot W. Beukers, Adriaan P. IJzerman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 577 KB

english, 2006

12

Functional grouping based on signatures in protein termini

Iris Bahir, Michal Linial

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 638 KB

english, 2006

13

Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains

Donard S. Dwyer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 227 KB

english, 2006

14

Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory

Aqeel Ahmed, Holger Gohlke

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 348 KB

english, 2006

15

Crystal structures of two putative phosphoheptose isomerases

Jayaraman Seetharaman, Kanagalaghatta R. Rajashankar, Veronica Solorzano, Ryan Kniewel, Christopher D. Lima, Jeffrey B. Bonanno, Stephen K. Burley, Subramanyam Swaminathan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 218 KB

english, 2006

16

Crystal structure of an RtcB homolog protein (PH1602-extein protein) from Pyrococcus horikoshii reveals a novel fold

Chiaki Okada, Yuki Maegawa, Min Yao, Isao Tanaka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 209 KB

english, 2006

17

Structural analysis of the transcriptional regulator homolog protein from Pyrococcus horikoshii OT3

Ui Okada, Naoki Sakai, Min Yao, Nobuhisa Watanabe, Isao Tanaka

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 192 KB

english, 2006

18

Chemical compound navigator: A web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds

M.D. Prasanna, Jiri Vondrasek, Alexander Wlodawer, H. Rodriguez, T. N. Bhat

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 544 KB

english, 2006

19

Terminal ion pairs stabilize the second β-hairpin of the B1 domain of protein G

Beatrice M. P. Huyghues-Despointes, Xiaotoa Qu, Jerry Tsai, J. Martin Scholtz

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 465 KB

english, 2006

20

Interdomain mobility in di-ubiquitin revealed by NMR

Yaroslav Ryabov, David Fushman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 512 KB

english, 2006

21

Conformational flexibility may explain multiple cellular roles of PEST motifs

Kuljeet Singh Sandhu, Debasis Dash

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 154 KB

english, 2006

22

Crystal structure of VC0702 at 2.0 Å: Conserved hypothetical protein from Vibrio cholerae

Shuisong Ni, Farhad Forouhar, Dirksen E. Bussiere, Howard Robinson, Michael A. Kennedy

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 809 KB

english, 2006

23

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis

Krzysztof J. Skowronek, Jan Kosinski, Janusz M. Bujnicki

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 551 KB

english, 2006

24

A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

Jonathan Myers, Greg Grothaus, Shivaram Narayanan, Alexey Onufriev

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 268 KB

english, 2006

25

Crystal structure of a putative HTH-type transcriptional regulator yxaF from Bacillus subtilis

Jayaraman Seetharaman, Desigan Kumaran, Jeffrey B. Bonanno, Stephen K. Burley, Subramanyam Swaminathan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 691 KB

english, 2006

26

Discrimination of outer membrane proteins using machine learning algorithms

M. Michael Gromiha, Makiko Suwa

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 82 KB

english, 2006

27

Effective handling of induced-fit motion in flexible docking

Miho Yamada Mizutani, Yoshihiro Takamatsu, Tazuko Ichinose, Kensuke Nakamura, Akiko Itai

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 610 KB

english, 2006

28

Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions

Carlos J. Camacho, Hui Ma, P. Christoph Champ

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 813 KB

english, 2006

29

Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

Inbal Halperin, Haim Wolfson, Ruth Nussinov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 549 KB

english, 2006

30

QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization

Zhigang Xu, Chi Zhang, Song Liu, Yaoqi Zhou

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 216 KB

english, 2006

31

Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: Thermodynamic and crystallographic studies

Evangelia G. Kapetaniou, Angelos Thanassoulas, Anatoly P. Dubnovitsky, George Nounesis, Anastassios C. Papageorgiou

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 676 KB

english, 2006

32

ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes

Mi-Ran Yun, R. Lavery, N. Mousseau, K. Zakrzewska, P. Derreumaux

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 370 KB

english, 2006

33

The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: An intermediate conformation with T-state and R-state features

Christine M. Lukacs, Nikos G. Oikonomakos, Robert L. Crowther, Li-Na Hong, R. Ursula Kammlott, Wayne Levin, Shirley Li, Chao-Min Liu, Debra Lucas-McGady, Sherrie Pietranico, Linda Reik

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 191 KB

english, 2006

34

Polyglutamine repeats and β-helix structure: Molecular dynamics study

Antonello Merlino, Luciana Esposito, Luigi Vitagliano

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 585 KB

english, 2006

35

Fold recognition and accurate sequence–structure alignment of sequences directing β-sheet proteins

Andrew V. McDonnell, Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen, Bonnie Berger

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 222 KB

english, 2006

36

Reducing CDK4/6-p16INK4a interface. Computational alanine scanning of a peptide bound to CDK6 protein

Óscar Villacañas, Jaime Rubio-Martinez

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 368 KB

english, 2006

37

Detailed microscopic study of the full zipA:FtsZ interface

I.S. Moreira, P.A. Fernandes, M.J. Ramos

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 498 KB

english, 2006

38

Modeling and functional analysis of AEBP1, a transcriptional repressor

Peter J. Lyons, Neil R. Mattatall, Hyo-Sung Ro

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 585 KB

english, 2006

39

Codep: Maximizing co-evolutionary interdependencies to discover interacting proteins

Elisabeth R. M. Tillier, Laurence Biro, Ginny Li, Desiree Tillo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 293 KB

english, 2006

40

Crystal structure of human protein tyrosine phosphatase 14 (PTPN14) at 1.65-Å resolution

Alastair J. Barr, Judit É. Debreczeni, Jeyanthy Eswaran, Stefan Knapp

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 234 KB

english, 2006

41

Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids

Yaw-Jen Liu, Chao-Sheng Cheng, Szu-Ming Lai, Ming-Pin Hsu, Ching-San Chen, Ping-Chiang Lyu

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.22 MB

english, 2006

42

Crystal structure of human spermidine/spermine N1-acetyltransferase (hSSAT): The first structure of a new sequence family of transferase homologous superfamily

Yong-Qun Zhu, De-Yu Zhu, Lei Yin, Ying Zhang, Clemens Vonrhein, Da-Cheng Wang

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 218 KB

english, 2006

43

Substructural cooperativity and parallel versus sequential events during protein unfolding

Lothar Reich, Thomas R. Weikl

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 341 KB

english, 2006

44

D-Trehalose/D-maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis: The binding of trehalose and maltose results in different protein conformational states

Petr Herman, Maria Staiano, Anna Marabotti, Antonio Varriale, Andrea Scirè, Fabio Tanfani, Jaroslav Vecer, Mose' Rossi, Sabato D'Auria

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 581 KB

english, 2006

45

Reconciling the “old” and “new” views of protein allostery: A molecular simulation study of chemotaxis Y protein (CheY)

Mark S. Formaneck, Liang Ma, Qiang Cui

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.69 MB

english, 2006

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