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1

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

Randy J. Read, Paul D. Adams, W. Bryan Arendall III, Axel T. Brunger, Paul Emsley, Robbie P. Joosten, Gerard J. Kleywegt, Eugene B. Krissinel, Thomas Lütteke, Zbyszek Otwinowski, Anastassis Perrakis,

Journal:

Year:

2011

Language:

english

File:

PDF, 1.44 MB

english, 2011

2

Recombinant cloning strategies for protein expression

Celie, Patrick HN, Parret, Annabel HA, Perrakis, Anastassis

Journal:

Current Opinion in Structural Biology

Year:

2016

Language:

english

File:

PDF, 539 KB

english, 2016

3

Ptprj is a candidate for the mouse colon-cancer susceptibility locus Scc1 and is frequently deleted in human cancers

Ruivenkamp, Claudia A.L., van Wezel, Tom, Zanon, Carlo, Stassen, Alphons P.M., Vlcek, Cestmir, Csikós, Tamás, Klous, Anita M., Tripodis, Nikos, Perrakis, Anastassis, Boerrigter, Lucie

Journal:

Nature Genetics

Year:

2002

Language:

english

File:

PDF, 197 KB

english, 2002

4

Insights into autotaxin: how to produce and present a lipid mediator

Moolenaar, Wouter H., Perrakis, Anastassis

Journal:

Nature Reviews Molecular Cell Biology

Year:

2011

Language:

english

File:

PDF, 1013 KB

english, 2011

5

The X-ray crystal structure of neuronal Sec1 from squid sheds new light on the role of this protein in exocytosis

Andreas Bracher, Anastassis Perrakis, Thomas Dresbach, Heinrich Betz, Winfried Weissenhorn

Journal:

Year:

2000

Language:

english

File:

PDF, 811 KB

english, 2000

6

Vasohibins encode tubulin detyrosinating activity

Nieuwenhuis, Joppe, Adamopoulos, Athanassios, Bleijerveld, Onno B., Mazouzi, Abdelghani, Stickel, Elmer, Celie, Patrick, Altelaar, Maarten, Knipscheer, Puck, Perrakis, Anastassis, Blomen, Vincent A.,

Journal:

Year:

2017

Language:

english

File:

PDF, 3.13 MB

english, 2017

7

Molecular, crystal and solution structure of a β-cyclodextrin complex with the bromide salt of 2-(3-dimethylaminopropyl)tricyclo[3.3.1.13,7]decan-2-ol, a potent antimicrobial drug

Anastassis Perrakis, Ekaterini Antoniadou-Vyza, Polyxeni Tsitsa, Victor S. Lamzin, Keith S. Wilson, Stavros J. Hamodrakas

Journal:

Carbohydrate Research

Year:

1999

Language:

english

File:

PDF, 461 KB

english, 1999

8

Insights into the DNA cleavage mechanism of human LINE-1 retrotransposon endonuclease

Kostas Repanas, Gloria Fuentes, Serge X. Cohen, Alexandre M. J. J. Bonvin, Anastassis Perrakis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 543 KB

english, 2009

9

Small is beautiful: protein micro-crystallography

Cusack, Stephen, Belrhali, Hassan, Bram, Andreas, Burghammer, Manfred, Perrakis, Anastassis, Riekel, Christian

Journal:

Natural Structural Biology

Year:

1998

Language:

english

File:

PDF, 252 KB

english, 1998

10

10.1038/29575

Schofield, Christopher J., Andersson, Inger, Valegård, Karin, van Scheltinga, Anke C. Terwisscha, Lloyd, Matthew D., Hara, Takane, Ramaswamy, S., Perrakis, Anastassis, Thompson, Andy, Lee, Hwei-Jen, B

Journal:

Year:

1998

Language:

english

File:

PDF, 512 KB

english, 1998

11

10.1038/35037523

Sixma, Titia K., Lamers, Meindert H., Perrakis, Anastassis, Enzlin, Jacqueline H., Winterwerp, Herrie H. K., de Wind, Niels

Journal:

Year:

2000

Language:

english

File:

PDF, 687 KB

english, 2000

12

10.1038/80763

Lamzin, Victor S., Perrakis, Anastassis

Journal:

Natural Structural Biology

Year:

2000

Language:

english

File:

PDF, 369 KB

english, 2000

13

10.1038/8263

Perrakis, Anastassis, Morris, Richard, Lamzin, Victor S.

Journal:

Natural Structural Biology

Year:

1999

Language:

english

File:

PDF, 521 KB

english, 1999

14

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

Langer, Gerrit, Cohen, Serge X, Lamzin, Victor S, Perrakis, Anastassis

Journal:

Nature Protocols

Year:

2008

Language:

english

File:

PDF, 342 KB

english, 2008

15

Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay–Sachs disease

Tews, Ivo, Perrakis, Anastassis, Oppenheim, Amos, Dauter, Zbigniew, Wilson, Keith S., Vorgias, Constantin E.

Journal:

Natural Structural Biology

Year:

1996

File:

PDF, 1.68 MB

1996

16

Structure and E3-ligase activity of the Ring–Ring complex of Polycomb proteins Bmi1 and Ring1b

Buchwald, Gretel, van der Stoop, Petra, Weichenrieder, Oliver, Perrakis, Anastassis, van Lohuizen, Maarten, Sixma, Titia K

Journal:

The EMBO Journal

Year:

2006

Language:

english

File:

PDF, 431 KB

english, 2006

17

Structural Basis for Ca2+ Regulation in the Na+/Ca2+ Exchanger

MARK HILGE, JAN AELEN, ANASTASSIS PERRAKIS, GEERTEN W. VUISTER

Journal:

Annals of the New York Academy of Sciences

Year:

2007

Language:

english

File:

PDF, 213 KB

english, 2007

18

Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA

van Pouderoyen, Gertie, Ketting, René F., Perrakis, Anastassis, Plasterk, Ronald H.A., Sixma, Titia K.

Journal:

The EMBO Journal

Year:

1997

Language:

english

File:

PDF, 700 KB

english, 1997

19

Polo-box domains confer target specificity to the Polo-like kinase family

Barbara C.M. van de Weerdt, Dene R. Littler, Rob Klompmaker, Angelina Huseinovic, Alex Fish, Anastassis Perrakis, René H. Medema

Journal:

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

Year:

2008

Language:

english

File:

PDF, 975 KB

english, 2008

20

Polo-like Kinase-1 Controls Proteasome-Dependent Degradation of Claspin during Checkpoint Recovery

Ivan Mamely, Marcel ATM van Vugt, Veronique AJ Smits, Jennifer I. Semple, Bennie Lemmens, Anastassis Perrakis, René H. Medema, Raimundo Freire

Journal:

Current Biology

Year:

2006

Language:

english

File:

PDF, 375 KB

english, 2006

21

Crystal Structure of the Targeting Endonuclease of the Human LINE-1 Retrotransposon

Oliver Weichenrieder, Kostas Repanas, Anastassis Perrakis

Journal:

Year:

2004

Language:

english

File:

PDF, 841 KB

english, 2004

22

Selectivity and Promiscuity in Eph Receptors

Anna-Pavlina G. Haramis, Anastassis Perrakis

Journal:

Year:

2006

Language:

english

File:

PDF, 71 KB

english, 2006

23

“Conditional Restraints”: Restraining the Free Atoms in ARP/wARP

Wijnand T.M. Mooij, Serge X. Cohen, Krista Joosten, Garib N. Murshudov, Anastassis Perrakis

Journal:

Year:

2009

Language:

english

File:

PDF, 418 KB

english, 2009

24

Crystal structure of a bacterial chitinase at 2.3 Å resolution

Anastassis Perrakis, Ivo Tews, Zbigniew Dauter, Amos B Oppenheim, Ilan Chet, Keith S Wilson, Constantin E Vorgias

Journal:

Year:

1994

Language:

english

File:

PDF, 1.54 MB

english, 1994

25

Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin

Ernst Schönbrunn, Stefan Sack, Susanne Eschenburg, Anastassis Perrakis, Florian Krekel, Nikolaus Amrhein, Eckhard Mandelkow

Journal:

Year:

1996

Language:

english

File:

PDF, 1.41 MB

english, 1996

26

Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications

Anastassis Perrakis, Christos Ouzounis, Keith S Wilson

Journal:

Folding and Design

Year:

1997

Language:

english

File:

PDF, 306 KB

english, 1997

27

The Crystal Structure of the Complexes of Concanavalin A with 4′-Nitrophenyl-α-d-mannopyranoside and 4′-Nitrophenyl-α-d-glucopyranoside

Panagiotis N. Kanellopoulos, Kyriaki Pavlou, Anastassis Perrakis, Bogos Agianian, Constantin E. Vorgias, Costas Mavrommatis, Maria Soufi, Paul A. Tucker, Stavros J. Hamodrakas

Journal:

Journal of Structural Biology

Year:

1996

Language:

english

File:

PDF, 2.32 MB

english, 1996

28

The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase

Saskia J.E. Suijkerbuijk, Teunis J.P. van Dam, G. Elif Karagöz, Eleonore von Castelmur, Nina C. Hubner, Afonso M.S. Duarte, Mathijs Vleugel, Anastassis Perrakis, Stefan G.D. Rüdiger, Berend Snel, Geer

Journal:

Developmental Cell

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

29

Investigating a macromolecular complex: The toolkit of methods

Anastassis Perrakis, Andrea Musacchio, Stephen Cusack, Carlo Petosa

Journal:

Journal of Structural Biology

Year:

2011

Language:

english

File:

PDF, 545 KB

english, 2011

30

From SPINE to SPINE-2 complexes and beyond

Anastassis Perrakis, Susan Daenke, David I. Stuart, Joel L. Sussman

Journal:

Journal of Structural Biology

Year:

2011

Language:

english

File:

PDF, 117 KB

english, 2011

31

Mechanism of USP7/HAUSP Activation by Its C-Terminal Ubiquitin-like Domain and Allosteric Regulation by GMP-Synthetase

Alex C. Faesen, Annette M.G. Dirac, Anitha Shanmugham, Huib Ovaa, Anastassis Perrakis, Titia K. Sixma

Journal:

Year:

2011

Language:

english

File:

PDF, 2.22 MB

english, 2011

32

Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger

Rodenko, Boris, Toebes, Mireille, Celie, Patrick H. N., Perrakis, Anastassis, Schumacher, Ton N. M., Ovaa, Huib

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 1.46 MB

english, 2009

33

UV-Induced Ligand Exchange in MHC Class I Protein Crystals

Celie, Patrick H. N., Toebes, Mireille, Rodenko, Boris, Ovaa, Huib, Perrakis, Anastassis, Schumacher, Ton N. M.

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 2.38 MB

english, 2009

34

Structure of NPP1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification

Silvia Jansen, Anastassis Perrakis, Chris Ulens, Claudia Winkler, Maria Andries, Robbie P. Joosten, Maarten Van Acker, Frank P. Luyten, Wouter H. Moolenaar, Mathieu Bollen

Journal:

Year:

2012

Language:

english

File:

PDF, 1.73 MB

english, 2012

35

Binding of the J-Binding Protein to DNA Containing Glucosylated hmU (Base J) or 5-hmC: Evidence for a Rapid Conformational Change upon DNA Binding

Heidebrecht, Tatjana, Fish, Alexander, von Castelmur, Eleonore, Johnson, Kenneth A., Zaccai, Giuseppe, Borst, Piet, Perrakis, Anastassis

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 2.45 MB

english, 2012

36

Structure–function relationships of autotaxin, a secreted lysophospholipase D

Hausmann, Jens, Perrakis, Anastassis, Moolenaar, Wouter H.

Journal:

Advances in Biological Regulation

Year:

2013

Language:

english

File:

PDF, 668 KB

english, 2013

37

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Tews, Ivo, Terwisscha van Scheltinga, Anke C., Perrakis, Anastassis, Wilson, Keith S., Dijkstra, Bauke W.

Journal:

Journal of the American Chemical Society

Year:

1997

Language:

english

File:

PDF, 309 KB

english, 1997

38

Use of Acetylcholine Binding Protein in the Search for Novel α7 Nicotinic Receptor Ligands. In Silico Docking, Pharmacological Screening, and X-ray Analysis †

Ulens, Chris, Akdemir, Atilla, Jongejan, Aldo, van Elk, Rene, Bertrand, Sonia, Perrakis, Anastassis, Leurs, Rob, Smit, August B., Sixma, Titia K., Bertrand, Daniel, de Esch, Iwan J. P.

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

39

Structure-Based Design of Novel Boronic Acid-Based Inhibitors of Autotaxin

Albers, Harald M. H. G., Hendrickx, Loes J. D., van Tol, Rob J. P., Hausmann, Jens, Perrakis, Anastassis, Ovaa, Huib

Journal:

Journal of Medicinal Chemistry

Year:

2011

Language:

english

File:

PDF, 3.97 MB

english, 2011

40

Evolutionary divergence and conservation of trypsin

Rypniewski, Wojciech R., Perrakis, Anastassis, Vorgias, Constantin E., Wilson, Keith S.

Journal:

Protein Engineering Design and Selection

Year:

1994

Language:

english

File:

PDF, 4.83 MB

english, 1994

41

The PDB_REDO server for macromolecular structure model optimization

Joosten, Robbie P., Long, Fei, Murshudov, Garib N., Perrakis, Anastassis

Journal:

Year:

2014

Language:

english

File:

PDF, 954 KB

english, 2014

42

Timely deposition of macromolecular structures is necessary for peer review

Joosten, Robbie P., Soueidan, Hayssam, Wessels, Lodewyk F. A., Perrakis, Anastassis

Journal:

Acta Crystallographica Section D Biological Crystallography

Year:

2013

Language:

english

File:

PDF, 2.39 MB

english, 2013

43

Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin

Hausmann, Jens, Keune, Willem-Jan, Hipgrave Ederveen, Agnes L., van Zeijl, Leonie, Joosten, Robbie P., Perrakis, Anastassis

Journal:

Journal of Structural Biology

Year:

2016

Language:

english

File:

PDF, 1.85 MB

english, 2016

44

Editorial overview: New constructs and expression of proteins

Meijers, Rob, Perrakis, Anastassis

Journal:

Current Opinion in Structural Biology

Year:

2016

Language:

english

File:

PDF, 121 KB

english, 2016

45

Structural basis of reversine selectivity in inhibiting Mps1 more potently than aurora B kinase

Hiruma, Yoshitaka, Koch, Andre, Dharadhar, Shreya, Joosten, Robbie P., Perrakis, Anastassis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 411 KB

english, 2016

46

Understanding inhibitor resistance in Mps1 kinase through novel biophysical assays and structures

Hiruma, Yoshitaka, Koch, Andre, Hazraty, Nazila, Tsakou, Foteini, Medema, Rene H., Joosten, Robbie P., Perrakis, Anastassis

Journal:

Journal of Biological Chemistry

Year:

2017

Language:

english

File:

PDF, 4.02 MB

english, 2017

47

Homology-based hydrogen bond information improves crystallographic structures in the PDB

van Beusekom, Bart, Touw, Wouter G., Tatineni, Mahidhar, Somani, Sandeep, Rajagopal, Gunaretnam, Luo, Jinquan, Gilliland, Gary L., Perrakis, Anastassis, Joosten, Robbie P.

Journal:

Protein Science

Year:

2017

Language:

english

File:

PDF, 1.52 MB

english, 2017

48

Glycerophosphodiesterase GDE2/GDPD5 affects pancreas differentiation in zebrafish

van Veen, Michiel, Mans, Laurie A., Matas-Rico, Elisa, van Pelt, Jason, Perrakis, Anastassis, Moolenaar, Wouter H., Haramis, Anna-Pavlina G.

Journal:

The International Journal of Biochemistry & Cell Biology

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

49

Lysophosphatidic acid produced by autotaxin acts as an allosteric modulator of its catalytic efficiency

Salgado-Polo, Fernando, Fish, Alex, Matsoukas, Minos-Timotheos, Heidebrecht, Tatjana, Keune, Willem-Jan, Perrakis, Anastassis

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 3.81 MB

english, 2018

50

Profilin 1 binding couples chloride intracellular channel protein CLIC4 to RhoA–mDia2 signaling and filopodium formation

Argenzio, Elisabetta, Klarenbeek, Jeffrey, Kedziora, Katarzyna M, Nahidiazar, Leila, Isogai, Tadamoto, Perrakis, Anastassis, Jalink, Kees, Moolenaar, Wouter H., Innocenti, Metello

Journal:

Journal of Biological Chemistry

Year:

2018

Language:

english

File:

PDF, 3.31 MB

english, 2018