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1

Blind predictions of protein interfaces by docking calculations in CAPRI

Marc F. Lensink, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.21 MB

english, 2010

2

Deviations from Standard Atomic Volumes as a Quality Measure for Protein Crystal Structures

Joan Pontius, Jean Richelle, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 548 KB

english, 1996

3

Interaction databases on the same page

Turinsky, Andrei L, Razick, Sabry, Turner, Brian, Donaldson, Ian M, Wodak, Shoshana J

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 239 KB

english, 2011

4

Docking, scoring, and affinity prediction in CAPRI

Lensink, Marc F., Wodak, Shoshana J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 436 KB

english, 2013

5

Viral Phylodynamics

Volz, Erik M., Koelle, Katia, Bedford, Trevor, Wodak, Shoshana

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 388 KB

english, 2013

6

Free Energy of Cavity Formation in Liquid Water and Hexane

Prévost, Martine, Oliveira, Isabel T., Kocher, Jean-Pierre, Wodak, Shoshana J.

Journal:

Journal of Physical Chemistry

Year:

1996

Language:

english

File:

PDF, 330 KB

english, 1996

7

Effect of nucleotide substrate binding on the pKa of catalytic residues in barnase

Gordon‐Beresford, Roland M.H., Van Belle, Daniel, Giraldo, Jesús, Wodak, Shoshana J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 1.39 MB

english, 1996

8

Identification of structural domains in proteins by a graph heuristic

Lorenz Wernisch, Marcel Hunting, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 211 KB

english, 1999

9

Reaction pathway for the quaternary structure change in hemoglobin

Joël Janin, Shoshana J. Wodak

Journal:

Year:

1985

Language:

english

File:

PDF, 990 KB

english, 1985

10

Detection of cavities in a set of interpenetrating spheres

Philippe Alard, Shoshana J. Wodak

Journal:

Journal of Computational Chemistry

Year:

1991

Language:

english

File:

PDF, 545 KB

english, 1991

11

Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa : Proposal for a proton pathway from the analysis of internal cavities

Olivier Radresa, Koji Ogata, Shoshana Wodak, Jean-Marie Ruysschaert, Erik Goormaghtigh

Journal:

Year:

2002

Language:

english

File:

PDF, 532 KB

english, 2002

12

Solution structure of the main α-amylase inhibitor from amaranth seeds

José C. Martins, Mohammed Enassar, Rudolph Willem, Jean-Michel Wieruzeski, Guy Lippens, Shoshana J. Wodak

Journal:

Year:

2001

Language:

english

File:

PDF, 2.61 MB

english, 2001

13

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae

Shuye Pu, Jim Vlasblom, Andrew Emili, Jack Greenblatt, Shoshana J. Wodak

Journal:

Year:

2007

Language:

english

File:

PDF, 766 KB

english, 2007

14

Analysis of zinc binding sites in protein crystal structures

Ian L. Alberts, Katalin Nadassy, Shoshana J. Wodak

Journal:

Protein Science

Year:

1998

Language:

english

File:

PDF, 7.92 MB

english, 1998

15

CAPRI: A Critical Assessment of PRedicted Interactions

Joël Janin, Kim Henrick, John Moult, Lynn Ten Eyck, Michael J. E. Sternberg, Sandor Vajda, Ilya Vakser, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 198 KB

english, 2003

16

Assessment of blind predictions of protein–protein interactions: Current status of docking methods

Raúl Méndez, Raphaël Leplae, Leonardo De Maria, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 689 KB

english, 2003

17

Progressive combinatorial algorithm for multiple structural alignments: Application to distantly related proteins

María Elena Ochagavía, Shoshana Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.98 MB

english, 2004

18

Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase

Jesús Giraldo, Leonardo De Maria, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 1.47 MB

english, 2004

19

Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures

Raúl Méndez, Raphaël Leplae, Marc F. Lensink, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 460 KB

english, 2005

20

Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: Implications for barnase catalysis

Maite Roca, Leonardo De Maria, Shoshana J. Wodak, Vicente Moliner, Iñaki Tuñón, Jesús Giraldo

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 475 KB

english, 2008

21

Docking and scoring protein complexes: CAPRI 3rd Edition

Marc F. Lensink, Raúl Méndez, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 543 KB

english, 2007

22

From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent

Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 65 KB

english, 2007

23

Role of the amino acid sequence in domain swapping of the B1 domain of protein G

Fernanda L. Sirota, Stephanie Héry-Huynh, Sebastian Maurer-Stroh, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.38 MB

english, 2008

24

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses

Tuan On, Xuejian Xiong, Shuye Pu, Andrei Turinsky, Yunchen Gong, Andrew Emili, Zhaolei Zhang, Jack Greenblatt, Shoshana J. Wodak, John Parkinson

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.35 MB

english, 2010

25

Docking and scoring protein interactions: CAPRI 2009

Marc F. Lensink, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 384 KB

english, 2010

26

Structural analysis of the 2.8 Å model of xylose isomerase from Actinoplanes missouriensis

Felix Rey, John Jenkins, Dr. Joël Janin, Ignace Lasters, Philippe Alard, Michel Classens, Gaston Matthyssens, Shoshana Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1988

Language:

english

File:

PDF, 933 KB

english, 1988

27

The design of idealized α/β-barrels: Analysis of β-sheet closure requirements

Ignace Lasters, Shoshana J. Wodak, Fredric Pio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1990

Language:

english

File:

PDF, 773 KB

english, 1990

28

Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins

Marianne J. Rooman, Dr. Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1991

Language:

english

File:

PDF, 1.01 MB

english, 1991

29

Sesam: A relational database for structure and sequence of macromolecules

Martina Huysmans, Jean Richelle, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1991

Language:

english

File:

PDF, 1.78 MB

english, 1991

30

Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features

Jean-Pierre Y. Scheerlinck, Dr. Ignace Lasters, Dr. Michel Claessens, Marc De Maeyer, Dr. Frederic Pio, Dr. Philippe Delhaise, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1992

Language:

english

File:

PDF, 1.53 MB

english, 1992

31

The quaternary structure of carbonmonoxy hemoglobin ypsilanti

Joël Janin, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1993

Language:

english

File:

PDF, 372 KB

english, 1993

32

Protein structure prediction by threading methods: Evaluation of current techniques

Christian M.-R. Lemer, Marianne J. Rooman, Shoshana J. Wodak

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 2.10 MB

english, 1995

33

Influence of ligand binding on the conformation of Torpedo californica acetylcholinesterase

Nathalie Boutonnet, Daniel Van Belle, Shoshana J. Wodak

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2001

Language:

english

File:

PDF, 696 KB

english, 2001

34

Identification of predictive sequence motifs limited by protein structure data base size

Rooman, Marianne J., Wodak, Shoshana J.

Journal:

Year:

1988

File:

PDF, 750 KB

1988

35

Extending molecular systematics to the third dimension

Wodak, Shoshana J.

Journal:

Natural Structural Biology

Year:

1996

File:

PDF, 522 KB

1996

36

PESCADOR: The PEptides in Solution ConformAtion Database: Online Resource

Anne Pajon, Wim F. Vranken, Maria Angeles Jimenez, Manuel Rico, Shoshana J. Wodak

Journal:

Journal of Biomolecular NMR

Year:

2002

Language:

english

File:

PDF, 549 KB

english, 2002

37

Next-generation protein engineering targets influenza

Wodak, Shoshana J

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

38

Brain abnormalities in patients with Beckwith–Wiedemann syndrome

Kate Gardiner, David Chitayat, Sanaa Choufani, Cheryl Shuman, Susan Blaser, Deborah Terespolsky, Sandra Farrell, Rosemary Reiss, Shoshana Wodak, Shuye Pu, Peter N. Ray, Berivan Baskin, Rosanna Weksber

Journal:

American Journal of Medical Genetics Part A

Year:

2012

Language:

english

File:

PDF, 403 KB

english, 2012

39

Activators of Cylindrical Proteases as Antimicrobials: Identification and Development of Small Molecule Activators of ClpP Protease

Elisa Leung, Alessandro Datti, Michele Cossette, Jordan Goodreid, Shannon E. McCaw, Michelle Mah, Alina Nakhamchik, Koji Ogata, Majida El Bakkouri, Yi-Qiang Cheng, Shoshana J. Wodak, Bryan T. Eger, Em

Journal:

Chemistry & Biology

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

40

Prediction of protein–protein interactions: the CAPRI experiment, its evaluation and implications

Shoshana J Wodak, Raúl Méndez

Journal:

Current Opinion in Structural Biology

Year:

2004

Language:

english

File:

PDF, 311 KB

english, 2004

41

The Third CAPRI Assessment Meeting Toronto, Canada, April 20–21, 2007

Joël Janin, Shoshana Wodak

Journal:

Year:

2007

Language:

english

File:

PDF, 301 KB

english, 2007

42

Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats

Andrey V Kajava, Gilbert Vassart, Shoshana J Wodak

Journal:

Year:

1995

Language:

english

File:

PDF, 1.47 MB

english, 1995

43

Properties of the protein matrix revealed by the free energy of cavity formation

Jean-Pierre Kocher, Martine Prévost, Shoshana J Wodak, Byungkook Lee

Journal:

Year:

1996

Language:

english

File:

PDF, 971 KB

english, 1996

44

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs

James Vlasblom, Shoshana J Wodak

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 759 KB

english, 2009

45

Relating destabilizing regions to known functional sites in proteins

Benoît H Dessailly, Marc F Lensink, Shoshana J Wodak

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.40 MB

english, 2007

46

Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets

Guillaume Launay, Raul Mendez, Shoshana Wodak, Thomas Simonson

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.03 MB

english, 2007

47

Factors Influencing the Ability of Knowledge-based Potentials to Identify Native Sequence-Structure Matches

Jean-Pierre A. Kocher, Marianne J. Rooman, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 1.01 MB

1994

48

Unfolding Simulations of the 85-102 β-Hairpin of Barnase

Luisa Pugliese, Martine Prévost, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 4.48 MB

english, 1995

49

Automatic Analysis of Protein Conformational Changes by Multiple Linkage Clustering

Nathalie S. Boutonnet, Marianne J. Rooman, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 1.61 MB

english, 1995

50

Automatic Classification and Analysis of αα-Turn Motifs in Proteins

René T. Wintjens, Marianne J. Rooman, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1996

Language:

english

File:

PDF, 2.28 MB

english, 1996