Volume 55; Issue 3

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Proteins: Structure, Function, and Bioinformatics
Volume 55; Issue 3

Proteins: Structure, Function, and Bioinformatics

Volume 55; Issue 3

1

Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model

Mathew C. Lee, Yong Duan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 170 KB

english, 2004

2

Protein secondary structure assignment through Voronoï tessellation

Franck Dupuis, Jean-François Sadoc, Jean-Paul Mornon

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 393 KB

english, 2004

3

Modeling structurally variable regions in homologous proteins with rosetta

Carol A. Rohl, Charlie E.M. Strauss, Dylan Chivian, David Baker

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 426 KB

english, 2004

4

Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 Å resolution

Robert Schwarzenbacher, Lukasz Jaroszewski, Frank von Delft, Polat Abdubek, Eileen Ambing, Tanja Biorac, Linda S. Brinen, Jaume M. Canaves, Jamison Cambell, Hsui-Ju Chiu, Xiaoping Dai, Ashley M. Deaco

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 596 KB

english, 2004

5

Evaluation of local structure alphabets based on residue burial

Rachel Karchin, Melissa Cline, Kevin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

6

NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis Reveals a distinct 5-helix bundle

Gaohua Liu, Dinesh K. Sukumaran, Duanxiang Xu, Yiwen Chiang, Thomas Acton, Sharon Goldsmith-Fischman, Barry Honig, Gaetano T. Montelione, Thomas Szyperski

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 165 KB

english, 2004

7

Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV

Yasuhiro Katsura, Mikako Shirouzu, Hiroto Yamaguchi, Ryuichiro Ishitani, Osamu Nureki, Seiki Kuramitsu, Hideyuki Hayashi, Shigeyuki Yokoyama

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.32 MB

english, 2004

8

Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase

Alice Grassick, Gerlind Sulzenbacher, Véronique Roig-Zamboni, Valérie Campanacci, Christian Cambillau, Yves Bourne

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 156 KB

english, 2004

9

Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 Å resolution

Robert Schwarzenbacher, Lukasz Jaroszewski, Frank von Delft, Polat Abdubek, Eileen Ambing, Tanja Biorac, Linda S. Brinen, Jaume M. Canaves, Jamison Cambell, Hsiu-Ju Chiu, Xiaoping Dai, Ashley M. Deaco

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 190 KB

english, 2004

10

X-ray structural and simulation analysis of a protein mutant: The value of a combined approach

Carla Mattos, Justin D. Cohen, David F. Green, Bruce Tidor, Martin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 157 KB

english, 2004

11

The determinants of carboxyl pKa values in turkey ovomucoid third domain

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 632 KB

english, 2004

12

The architecture of the binding site in redox protein complexes: Implications for fast dissociation

Peter B. Crowley, Maria Arménia Carrondo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 203 KB

english, 2004

13

Crystal structure of human L-xylulose reductase holoenzyme: Probing the role of Asn107 with site-directed mutagenesis

Ossama El-Kabbani, Shuhei Ishikura, Connie Darmanin, Vincenzo Carbone, Roland P.-T. Chung, Noriyuki Usami, Akira Hara

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 324 KB

english, 2004

14

Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models

Cristian Micheletti, Paolo Carloni, Amos Maritan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 228 KB

english, 2004

15

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

Mihaly Mezei, Patrick J. Fleming, Rajgopal Srinivasan, George D. Rose

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 289 KB

english, 2004

16

Unfolded state of polyalanine is a segmented polyproline II helix

Alex Kentsis, Mihaly Mezei, Tatyana Gindin, Roman Osman

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 517 KB

english, 2004

17

On the functional significance of electron density protein structure alignments

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 193 KB

english, 2004

18

Atomic insight into the CD4 binding-induced conformational changes in HIV-1 gp120

Shang-Te D. Hsu, Alexandre M.J.J. Bonvin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.03 MB

english, 2004

19

A set of homology models of pore loop domain of six eukaryotic voltage-gated potassium channels Kv1.1-Kv1.6

Hsuan-Liang Liu, Jin-Chung Lin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 450 KB

english, 2004

20

Folding of β/α-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (β/α)8-barrel

Anshuman Shukla, Purnananda Guptasarma

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 204 KB

english, 2004

21

A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease

Sonia Vega, Lin-Woo Kang, Adrian Velazquez-Campoy, Yoshiaki Kiso, L. Mario Amzel, Ernesto Freire

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 291 KB

english, 2004

22

Investigation of glucose binding sites on insulin

Vincent Zoete, Markus Meuwly, Martin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 745 KB

english, 2004

23

Topological thermal instability and length of proteins

Raffaella Burioni, Davide Cassi, Fabio Cecconi, Angelo Vulpiani

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 131 KB

english, 2004

24

Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis

Alessandro Porrello, Silvia Soddu, Joseph P. Zbilut, Marco Crescenzi, Alessandro Giuliani

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 407 KB

english, 2004

25

Is histoaspartic protease a serine protease with a pepsin-like fold?

N. Andreeva, P. Bogdanovich, I. Kashparov, M. Popov, M. Stengach

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 533 KB

english, 2004

26

The 1.59 Å resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima

Frances Park, Ketan Gajiwala, Brian Noland, Lydia Wu, Dongmei He, Janessa Molinari, Kim Loomis, Barbra Pagarigan, Peggy Kearins, Jon Christopher, Tom Peat, John Badger, Jorg Hendle, Johann Lin, Sean B

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 248 KB

english, 2004

27

Crystal structure of YIGZ, a conserved hypothetical protein from Escherichia coli k12 with a novel fold

Frances Park, Ketan Gajiwala, Galina Eroshkina, Eva Furlong, Dongmei He, Yelena Batiyenko, Rich Romero, Jon Christopher, John Badger, Jorg Hendle, Johann Lin, Tom Peat, Sean Buchanan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 257 KB

english, 2004

28

Recognition of coarse-grained protein tertiary structure

Timothy Lezon, Jayanth R. Banavar, Amos Maritan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 160 KB

english, 2004

29

CHOP proteins into structural domain-like fragments

Jinfeng Liu, Burkhard Rost

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 482 KB

english, 2004

30

The low barrier hydrogen bond (LBHB) proposal revisited: The case of the Asp ··· His pair in serine proteases

Claudia N. Schutz, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 220 KB

english, 2004

31

DRESS: a database of REfined solution NMR structures

Sander B. Nabuurs, Aart J. Nederveen, Wim Vranken, Jurgen F. Doreleijers, Alexandre M.J.J. Bonvin, Geerten W. Vuister, Gert Vriend, Christian A.E.M. Spronk

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 202 KB

english, 2004

32

Crystal structure of the conserved hypothetical protein TT1380 from Thermus thermophilus HB8

Takashi Wada, Mikako Shirouzu, Takaho Terada, Yuki Kamewari, Sam-Yong Park, Jeremy R.H. Tame, Seiki Kuramitsu, Shigeyuki Yokoyama

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 150 KB

english, 2004

33

NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer

Matthias Stehr, Ylva Lindqvist

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 437 KB

english, 2004

34

Predicting protein quaternary structure by pseudo amino acid composition

Kuo-Chen Chou, Yu-Dong Cai

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

File:

PDF, 25 KB

2004

35

Assessment of homology-based predictions in CASP5

Anna Tramontano, Veronica Morea

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 34 KB

english, 2004

36

Crystal structure of Homo sapiens protein hp14.5

Babu A. Manjasetty, Heinrich Delbrück, Dinh-Trung Pham, Uwe Mueller, Martin Fieber-Erdmann, Christoph Scheich, Volker Sievert, Konrad Büssow, Frank H. Niesen, Wilhelm Weihofen, Bernhard Loll, Wolfram

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 30 KB

english, 2004

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