A. Perrakis

发表

Automated protein model building combined with iterative structure refinement

Anastassis Perrakis, Victor S. Lamzin, R. Morris, 1999, Nature Structural Biology.

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

Serge X. Cohen, V. Lamzin, A. Perrakis, 2008, Nature Protocols.

Investigating a macromolecular complex: the toolkit of methods.

S. Cusack, A. Musacchio, C. Petosa, 2011, Journal of structural biology.

Assessment of automatic ligand building in ARP/wARP

V. Lamzin, A. Perrakis, G. Langer, 2006, Acta crystallographica. Section D, Biological crystallography.

Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.

O. Weichenrieder, A. Perrakis, K. Repanas, 2004, Structure.

Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease

O. Weichenrieder, A. Perrakis, K. Repanas, 2007, Nucleic acids research.

Autotaxin: structure-function and signaling

A. Perrakis, W. Moolenaar, 2014, Journal of Lipid Research.

iNEXT: a European facility network to stimulate translational structural biology

J. Ellenberg, H. Schwalbe, D. Stuart, 2018, FEBS letters.

The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.

Mathijs Vleugel, Berend Snel, Anastassis Perrakis, 2012, Developmental cell.

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

Oliver Weichenrieder, Anastassis Perrakis, T. Sixma, 2006, The EMBO journal.

Crystals, x-rays and proteins: comprehensive protein crystallography, by Dennis Sherwood and Jon Cooper

A. Perrakis, E. von Castelmur, 2011 .

Crystal structure of a bacterial chitinase at 2.3 A resolution.

K S Wilson, Z Dauter, A Perrakis, 1994, Structure.

wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models.

V S Lamzin, K S Wilson, A Perrakis, 1997, Acta crystallographica. Section D, Biological crystallography.

RNA-Binding Protein Dnd1 Inhibits MicroRNA Access to Target mRNA

Reuven Agami, Erez Raz, Anastassis Perrakis, 2007, Cell.

Use of acetylcholine binding protein in the search for novel alpha7 nicotinic receptor ligands. In silico docking, pharmacological screening, and X-ray analysis.

D. Bertrand, T. Sixma, I. D. de Esch, 2009, Journal of medicinal chemistry.

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

Serge X. Cohen, A. Bonvin, G. Fuentes, 2009, Proteins.

Breaking good resolutions with ARP/wARP.

Victor S Lamzin, Serge X. Cohen, Anastassis Perrakis, 2004, Journal of synchrotron radiation.

Imaging Autotaxin In Vivo with 18F-Labeled Positron Emission Tomography Ligands.

Steven H. Liang, L. Josephson, A. Perrakis, 2021, Journal of medicinal chemistry.

Eukaryotic expression: developments for structural proteomics

L. Gustafsson, T. Sixma, G. Schneider, 2006, Acta crystallographica. Section D, Biological crystallography.

Assembly of protein complexes by coexpression in prokaryotic and eukaryotic hosts: an overview.

Christophe Romier, Anastassis Perrakis, C. Romier, 2008, Methods in molecular biology.

Mammalian cell expression, purification, crystallization and microcrystal data collection of autotaxin/ENPP2, a secreted mammalian glycoprotein

G. Evans, E. Christodoulou, A. Perrakis, 2010, Acta crystallographica. Section F, Structural biology and crystallization communications.

Expression of protein complexes using multiple Escherichia coli protein co-expression systems: a benchmarking study.

R. Owens, Y. Peleg, K. Büssow, 2011, Journal of structural biology.

Mechanism of USP7/HAUSP activation by its C-terminal ubiquitin-like domain and allosteric regulation by GMP-synthetase.

T. Sixma, H. Ovaa, A. Faesen, 2011, Molecular cell.

A global Ramachandran score identifies protein structures with unlikely stereochemistry

P. Adams, P. Afonine, N. Moriarty, 2020, bioRxiv.

Structure of NPP1, an ectonucleotide pyrophosphatase/phosphodiesterase involved in tissue calcification.

F. Luyten, M. Bollen, C. Ulens, 2012, Structure.

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

R. Joosten, A. Perrakis, A. Koch, 2016, Proteins.

Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling

M. Ubbink, G. Kops, A. Perrakis, 2015, Science.

Cdt1 and geminin in DNA replication initiation.

A. Perrakis, C. Caillat, 2012, Sub-cellular biochemistry.

Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2 E3 ligase activity to Cdt1

T. Ishii, A. Perrakis, Tatsuro S. Takahashi, 2018, Life Science Alliance.

Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2 E3 ligase activity to Cdt1

T. Ishii, A. Perrakis, Tatsuro S. Takahashi, 2018, bioRxiv.

The Polybasic Insertion in Autotaxin α Confers Specific Binding to Heparin and Cell Surface Heparan Sulfate Proteoglycans*

Xander M R van Wijk, A. Fish, T. V. van Kuppevelt, 2012, The Journal of Biological Chemistry.

The domain architecture of the protozoan protein J-DNA–binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity

Wouter G. Touw, J. Beijnen, I. Phan, 2019, The Journal of Biological Chemistry.

The domain architecture of JBP1 suggests synergy between J-base DNA binding and thymidine hydroxylase activity

Wouter G. Touw, J. Beijnen, I. Phan, 2018 .

Secreted autotaxin through LPA suppresses chemotaxis and tumor infiltration of CD8+ T Cells

T. Schumacher, J. Koster, J. Haanen, 2020 .

University of Groningen Glycerophosphodiesterase GDE2 Promotes Neuroblastoma Differentiation through Glypican Release and Is a Marker of Clinical Outcome Matas-Rico,

M. Weerts, B. Giepmans, R. Medema, 2019 .

Glycerophosphodiesterase GDE2 Promotes Neuroblastoma Differentiation through Glypican Release and Is a Marker of Clinical Outcome.

M. Weerts, B. Giepmans, R. Medema, 2016, Cancer cell.

Building and rebuilding N-glycans in protein structure models

P. Emsley, R. Joosten, M. Hekkelman, 2019, Acta crystallographica. Section D, Structural biology.

Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations.

Roland A. Pache, B. Séraphin, P. Aloy, 2010, Structure.

The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase

R. Hausinger, P. Borst, D. Rigden, 2007, Nucleic acids research.

Posttranslational modification of microtubules by the MATCAP detyrosinase

T. Brummelkamp, A. Perrakis, S. Taraviras, 2022, Science.

Selectivity and promiscuity in Eph receptors.

A. Perrakis, Anna-Pavlina G Haramis, Anna-Pavlina G. Haramis, 2006, Structure.

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.

P. Adams, P. Afonine, N. Moriarty, 2020, Structure.

Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1–SVBP

T. Brummelkamp, M. Altelaar, A. Perrakis, 2019, Nature Structural & Molecular Biology.

Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with a Discrete Binding Mode.

Lisa M. Miller, Willem-Jan Keune, A. Perrakis, 2017, Journal of medicinal chemistry.

Small Molecule Inhibitor Targeting CDT1/Geminin Protein Complex Promotes DNA Damage and Cell Death in Cancer Cells

D. Egan, Joe D. Lewis, A. Fish, 2022, Frontiers in Pharmacology.

Structure‐Function Studies on the Chitinolytic Enzymes of Serratia marcescens Chitinase and Chitobiase

I. Tews, C. Vorgias, A. Perrakis, 1996, Annals of the New York Academy of Sciences.

Supplemental Information The Vertebrate Mitotic Checkpoint Protein BUBR 1 Is an Unusual Pseudokinase

Teunis J. P. van Dam, B. Snel, S. Rüdiger, 2012 .

Implementation of semi-automated cloning and prokaryotic expression screening: the impact of SPINE.

Raymond J Owens, Pedro M Alzari, C Cambillau, 2006, Acta crystallographica. Section D, Biological crystallography.

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

Serge X. Cohen, W. Mooij, G. Murshudov, 2009, Structure.

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

W. Weissenhorn, A. Bracher, T. Dresbach, 2000, Structure.

Structure-function relationships of autotaxin, a secreted lysophospholipase D.

A. Perrakis, W. Moolenaar, Jens Hausmann, 2013, Advances in biological regulation.

Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling

Willem-Jan Keune, A. Morris, R. Joosten, 2016, Nature Communications.

Crystal structure of the retinoblastoma tumor suppressor protein bound to E2F and the molecular basis of its regulation

M. Burghammer, S. Gamblin, R. Marmorstein, 2003, Proceedings of the National Academy of Sciences of the United States of America.

The Structural Binding Mode of the Four Autotaxin Inhibitor Types that Differentially Affect Catalytic and Non-Catalytic Functions

A. Perrakis, Fernando Salgado-Polo, 2019, Cancers.

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

A. Joachimiak, Z. Otwinowski, A. Perrakis, 2000, Structure.

Glycerophosphodiesterase GDE2/GDPD5 affects pancreas differentiation in zebrafish.

A. Perrakis, W. Moolenaar, Anna-Pavlina G Haramis, 2018, The international journal of biochemistry & cell biology.

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.

P. Borst, Kenneth A. Johnson, A. Fish, 2012, Journal of the American Chemical Society.

The structural basis for recognition of base J containing DNA by a novel DNA binding domain in JBP1

M. J. Chalmers, P. Griffin, P. Borst, 2011, Nucleic acids research.

Dynamic Kinetochore Size Regulation Promotes Microtubule Capture and Chromosome Biorientation in Mitosis

J. Carazo, A. Musacchio, R. Melero, 2018, Nature Cell Biology.

STRUCTURE-FUNCTION RELATIONSHIPS OF AUTOTAXIN GENERAL INTRODUCTION: STRUCTURE-FUNCTION RELATIONSHIPS OF AUTOTAXIN

A. Perrakis, W. Moolenaar, Jens Hausmann, 2013 .

Autotaxin facilitates selective LPA receptor signaling

A. Perrakis, W. Moolenaar, Fernando Salgado-Polo, 2022, bioRxiv.

A type IV Autotaxin inhibitor ameliorates acute liver injury and nonalcoholic steatohepatitis

A. Perrakis, Ruchi Bansal, Fernando Salgado-Polo, 2022, EMBO molecular medicine.

A type IV Autotaxin inhibitor ameliorates acute liver injury and non-alcoholic steatohepatitis in mice

A. Perrakis, Ruchi Bansal, Fernando Salgado-Polo, 2022, bioRxiv.

Crystal structure of the Phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain.

A. Perrakis, E. von Castelmur, I. Cornaciu, 2022, Journal of structural biology.

Inhibition of Autotaxin by Lysophosphatidic Acid and Sphingosine 1-Phosphate*

K. Kikuchi, J. Goding, T. Nagano, 2005, Journal of Biological Chemistry.

Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin.

Willem-Jan Keune, R. Joosten, A. Perrakis, 2016, Journal of structural biology.

Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies.

Christophe Romier, Tamar Unger, Joel L Sussman, 2006, Acta crystallographica. Section D, Biological crystallography.

First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value.

T. Sixma, G. Schneider, J. Sussman, 2006, Acta crystallographica. Section D, Biological crystallography.

Sequence-dependent trafficking and activity of GDE2, a GPI-specific phospholipase promoting neuronal differentiation

K. Jalink, A. Perrakis, B. van den Broek, 2020, Journal of Cell Science.

Neuronal differentiation through GPI-anchor cleavage by GDE2: regulation via sequence-dependent trafficking

M. Veen, B. V. D. Broek, A. Perrakis, 2019 .

Sequence-dependent trafficking of GDE2, a GPI-specific phospholipase promoting neuronal differentiation

M. Veen, B. V. D. Broek, A. Perrakis, 2019, bioRxiv.

AlphaFill: enriching AlphaFold models with ligands and cofactors

R. Joosten, M. Hekkelman, A. Perrakis, 2022, Nature Methods.

Autotaxin impedes anti-tumor immunity by suppressing chemotaxis and tumor infiltration of CD8+ T cells

T. Schumacher, J. Koster, J. Haanen, 2020, bioRxiv.

ARP/wARP and molecular replacement.

V S Lamzin, K S Wilson, M Harkiolaki, 2001, Acta crystallographica. Section D, Biological crystallography.

Glucosylated Hydroxymethyluracil, DNA Base J, Prevents Transcriptional Readthrough in Leishmania

P. Myler, B. Steensel, P. Borst, 2012, Cell.

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

H. Ovaa, A. Perrakis, Loes Hendrickx, 2011, Journal of medicinal chemistry.

Structure of a cephalosporin synthase

M. D. Lloyd, J. Hajdu, I. Andersson, 1998, Nature.

The crystal structure of DNA mismatch repair protein MutS binding to a G·T mismatch

Anastassis Perrakis, Titia K. Sixma, M. Lamers, 2000, Nature.

Molecular, crystal and solution structure of a beta-cyclodextrin complex with the bromide salt of 2-(3-dimethylaminopropyl)tricyclo[3.3.1.1(3,7)]decan-2-ol, a potent antimicrobial drug.

S. Hamodrakas, K. Wilson, V. Lamzin, 1999, Carbohydrate research.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

Anastassis Perrakis, Gert Vriend, Krista Joosten, 2011, Bioinform..

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

Randy J. Read, Paul D. Adams, Gerard J. Kleywegt, 2011, Structure.

AlphaFill: enriching the AlphaFold models with ligands and co-factors

R. Joosten, M. Hekkelman, A. Perrakis, 2021, bioRxiv.

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

Jinquan Luo, Gary L Gilliland, Bart van Beusekom, 2017, bioRxiv.

Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.

A Teplyakov, K S Wilson, A Perrakis, 1996, The EMBO journal.

Evolutionary divergence and conservation of trypsin.

K S Wilson, A Perrakis, K. Wilson, 1994, Protein engineering.

Two β-Lactamase Variants with Reduced Clavulanic Acid Inhibition Display Different Millisecond Dynamics

Misbha Ud Din Ahmad, M. Ubbink, A. Perrakis, 2021, Antimicrobial agents and chemotherapy.

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

K. Jalink, A. Perrakis, K. Kedziora, 2018, The Journal of Biological Chemistry.

CLIC4 is regulated by RhoA-mDia2 signaling through Profilin-1 binding to modulate filopodium length

K. Jalink, A. Perrakis, K. Kedziora, 2018, bioRxiv.

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

Zbigniew Dauter, Keith S. Wilson, Anastassis Perrakis, 1996, Nature Structural Biology.

The MPS1 kinase NTE region has helical propensity and preferred conformations towards the TPR domain

Wouter G. Touw, M. Ubbink, G. Kops, 2020, bioRxiv.

Tryptophan depletion results in tryptophan-to-phenylalanine substitutants

Remco Nagel, R. Agami, D. Peeper, 2022, Nature.

Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence

P. Aloy, Amelie Stein, R. Medema, 2010, Nucleic acids research.

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

R. Medema, A. Fish, D. Littler, 2008, Biochimica et biophysica acta.

Target highlights in CASP14: Analysis of models by structure providers

K. Fidelis, J. Moult, J. Tainer, 2021, Proteins.

Dynamic Kinetochore Size Regulation Promotes Microtubule Capture and Chromosome Biorientation in Mitosis

J. Carazo, A. Musacchio, R. Melero, 2018, bioRxiv.

PLA2G16 represents a switch between entry and clearance of Picornaviridae

J. Carette, T. Brummelkamp, J. Staring, 2017, Nature.

Conformational transitions of the mitotic adaptor Spindly underlie its interaction with Dynein and Dynactin

I. Vetter, A. Musacchio, A. Carter, 2022, bioRxiv.

Interactions between N-terminal Modules in MPS1 Enable Spindle Checkpoint Silencing.

G. Kops, A. Perrakis, E. Tromer, 2019, Cell reports.

A TPR domain–containing N-terminal module of MPS1 is required for its kinetochore localization by Aurora B

B. Snel, D. Littler, G. Kops, 2013, The Journal of cell biology.

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

Cestmir Vlcek, Anastassis Perrakis, Tom van Wezel, 2002, Nature Genetics.

Recombinant cloning strategies for protein expression.

Anastassis Perrakis, A. Perrakis, A. Parret, 2016, Current opinion in structural biology.

New restraints and validation approaches for nucleic acid structures in PDB-REDO

Xiang-Jun Lu, S. Velankar, R. Joosten, 2021, Acta crystallographica. Section D, Structural biology.

Structural basis for substrate discrimination and integrin binding by autotaxin

Anastassis Perrakis, Tao Wu, Karl Harlos, 2010, Nature Structural &Molecular Biology.

The PDB_REDO server for macromolecular structure model optimization

Fei Long, Robbie P. Joosten, Anastassis Perrakis, 2014, IUCrJ.

ARP/wARP and molecular replacement: the next generation

Fei Long, Serge X. Cohen, Anastassis Perrakis, 2007, Acta crystallographica. Section D, Biological crystallography.

AI revolutions in biology

T. Sixma, A. Perrakis, 2021, EMBO reports.

Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates.

M. Lamers, H. Winterwerp, T. Sixma, 2003, Nucleic acids research.

Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy.

Janet Newman, David Egan, Joel L Sussman, 2005, Acta crystallographica. Section D, Biological crystallography.

The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer That Inhibits Geminin Function in DNA Replication Licensing*

J. Blow, A. Perrakis, P. J. Gillespie, 2013, The Journal of Biological Chemistry.

Idas, a Novel Phylogenetically Conserved Geminin-related Protein, Binds to Geminin and Is Required for Cell Cycle Progression*

A. Perrakis, I. Symeonidou, S. Taraviras, 2011, The Journal of Biological Chemistry.

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

C. Ouzounis, K. Wilson, A. Perrakis, 1997, Folding & design.

ARP/wARP and automatic interpretation of protein electron density maps.

Richard J Morris, Anastassis Perrakis, Victor S Lamzin, 2003, Methods in enzymology.

Data Mining of Macromolecular Structures.

Bart van Beusekom, Anastassis Perrakis, Robbie P Joosten, 2016, Methods in molecular biology.

CCD 2: design constructs for protein expression, the easy way

A. G. Murachelli, A. Perrakis, George Damaskos, 2021, Acta crystallographica. Section D, Structural biology.

ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments

Anastassis Perrakis, Wijnand T. M. Mooij, Eirini Mitsiki, 2009, Nucleic Acids Res..

Developments in the CCP4 molecular-graphics project.

Anastassis Perrakis, Eugene Krissinel, Kevin Cowtan, 2004, Acta crystallographica. Section D, Biological crystallography.

A knowledge-driven approach for crystallographic protein model completion

Krista Joosten, Serge X. Cohen, Anastassis Perrakis, 2008, Acta crystallographica. Section D, Biological crystallography.

Negative regulation of urokinase receptor activity by a GPI-specific phospholipase C in breast cancer cells

K. Jalink, N. Sidenius, A. Perrakis, 2017, eLife.

Negative regulation of uPAR activity by a GPI-specific phospholipase C

K. Jalink, N. Sidenius, A. Perrakis, 2016, bioRxiv.

The crystal structure of the complexes of concanavalin A with 4'-nitrophenyl-alpha-D-mannopyranoside and 4'-nitrophenyl-alpha-D-glucopyranoside.

P. Tucker, B. Agianian, S. Hamodrakas, 1996, Journal of structural biology.

Vasohibins encode tubulin detyrosinating activity

T. Brummelkamp, Abdelghani Mazouzi, P. Knipscheer, 2017, Science.

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

T. Sixma, R. Plasterk, R. Ketting, 1997, The EMBO journal.

Crystal Structure of Murine/Human Ubc9 Provides Insight into the Variability of the Ubiquitin-conjugating System*

A Perrakis, T. Sixma, G. Hateboer, 1997, The Journal of Biological Chemistry.

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Structure elucidation of beta-mannanase: from the electron-density map to the DNA sequence.

J. Abrahams, K. Piontek, S. Gloor, 2001, Acta crystallographica. Section D, Biological crystallography.

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

Mark J van Raaij, Liang Tong, Torsten Schwede, 2011, Proteins.

Supplemental Information Mechanism of USP 7 / HAUSP Activation by Its C-Terminal Ubiquitin-like Domain and Allosteric Regulation by GMP-Synthetase

T. Sixma, H. Ovaa, A. Faesen, 2011 .

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Keith S. Wilson, Anastassis Perrakis, Ivo Tews, 1997 .

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

Anastassis Perrakis, A. Perrakis, W. Moolenaar, 2011, Nature Reviews Molecular Cell Biology.

Structure and function of the ecto-nucleotide pyrophosphatase/phosphodiesterase (ENPP) family: Tidying up diversity

A. Perrakis, W. Moolenaar, Fernando Salgado-Polo, 2021, The Journal of biological chemistry.

Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing

R. Medema, D. Svergun, J. Blow, 2009, Proceedings of the National Academy of Sciences.

Accelerated X-ray structure elucidation of a 36 kDa muramidase/transglycosylase using wARP.

K. H. Kalk, B. Dijkstra, V. Lamzin, 1998, Acta crystallographica. Section D, Biological crystallography.

The first step of peptide selection in antigen presentation by MHC class I molecules

Jacques Neefjes, Anastassis Perrakis, Robbie P Joosten, 2015, Proceedings of the National Academy of Sciences.

Class I major histocompatibility complexes loaded by a periodate trigger.

T. Schumacher, B. Rodenko, H. Ovaa, 2009, Journal of the American Chemical Society.

UV-induced ligand exchange in MHC class I protein crystals.

T. Schumacher, B. Rodenko, H. Ovaa, 2009, Journal of the American Chemical Society.

Modeling and Experimental Validation of the Binary Complex of the Plectin Actin-binding Domain and the First Pair of Fibronectin Type III (FNIII) Domains of the β4 Integrin*

A. Sonnenberg, K. Wilhelmsen, J. M. de Pereda, 2005, Journal of Biological Chemistry.

The G132S Mutation Enhances the Resistance of Mycobacterium tuberculosis β-Lactamase against Sulbactam

Misbha Ud Din Ahmad, M. Ubbink, A. Perrakis, 2021, Biochemistry.

Characterization and structure determination of a llama-derived nanobody targeting the J-base binding protein 1.

E. Pardon, J. Steyaert, A. Fish, 2018, Acta crystallographica. Section F, Structural biology communications.

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

A. Fish, A. Perrakis, Minos-Timotheos Matsoukas, 2018, The Journal of Biological Chemistry.

Small is beautiful: protein micro-crystallography

Manfred Burghammer, Anastassis Perrakis, Christian Riekel, 1998, Nature Structural Biology.

Molecular and crystal structure of 2-amino-6-dimethylamino-4-(tricyclo[3.3.1.13, 7]dec-1-yl) methyl-1,3,5-triazine

A. Camerman, N. Camerman, S. Hamodrakas, 1993 .

ARP/wARP's model-building algorithms. I. The main chain.

Richard J Morris, Anastassis Perrakis, Victor S Lamzin, 2002, Acta crystallographica. Section D, Biological crystallography.

PDB_REDO: constructive validation, more than just looking for errors

Krista Joosten, Robbie P. Joosten, Anastassis Perrakis, 2012, Acta crystallographica. Section D, Biological crystallography.

Structure of human CLIC3 at 2 Å resolution

P. Curmi, D. Littler, S. Breit, 2010, Proteins.

Ca2+ regulation in the Na+/Ca2+ exchanger features a dual electrostatic switch mechanism

G. W. Vuister, A. Perrakis, J. Aelen, 2009, Proceedings of the National Academy of Sciences.

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

G. W. Vuister, A. Perrakis, J. Aelen, 2007, Annals of the New York Academy of Sciences.

Enabling high-throughput ligation-independent cloning and protein expression for the family of ubiquitin specific proteases.

T. Sixma, D. Littler, E. Christodoulou, 2011, Journal of structural biology.

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

Anastassis Perrakis, Jennifer I. Semple, M. V. Vugt, 2006, Current Biology.

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins

A. Fish, A. Perrakis, S. Taraviras, 2015, Acta crystallographica. Section D, Biological crystallography.

Towards complete validated models in the next generation of ARP/wARP.

Richard J Morris, Anastassis Perrakis, Victor S Lamzin, 2004, Acta crystallographica. Section D, Biological crystallography.

Protein microcrystals and the design of a microdiffractometer: current experience and plans at EMBL and ESRF/ID13.

F Cipriani, S Cusack, A Perrakis, 1999, Acta crystallographica. Section D, Biological crystallography.

Characterisation and structure determination of a llama-derived nanobody targeting the J-base binding protein 1

E. Pardon, J. Steyaert, A. Fish, 2018, bioRxiv.

Homology-based loop modeling yields more complete crystallographic protein structures

Bart van Beusekom, Krista Joosten, Anastassis Perrakis, 2018, bioRxiv.

SPINE bioinformatics and data‐management aspects of high‐throughput structural biology

A. Rachedi, R. J. Morris, C. Cambillau, 2006, Acta crystallographica. Section D, Biological crystallography.

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

Mahidhar Tatineni, Anastassis Perrakis, Jinquan Luo, 2017, bioRxiv.

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators

A. Perrakis, S. Macdonald, C. Jamieson, 2022, Journal of medicinal chemistry.

SPINE workshop on automated X-ray analysis: a progress report.

G N Murshudov, A Muller, K D Cowtan, 2006, Acta crystallographica. Section D, Biological crystallography.

Conserved residues Glu37 and Trp229 play an essential role in protein folding of β‐lactamase

M. Ubbink, A. Perrakis, A. Chikunova, 2020, The FEBS journal.

Native mass spectrometry provides direct evidence for DNA mismatch-induced regulation of asymmetric nucleotide binding in mismatch repair protein MutS

Serge X. Cohen, J. Lebbink, H. Winterwerp, 2011, Nucleic acids research.

LAHMA: structure analysis through local annotation of homology-matched amino acids

R. Joosten, M. Hekkelman, A. Perrakis, 2021, Acta crystallographica. Section D, Structural biology.

West-Life: A Virtual Research Environment for structural biology

Andrea Giachetti, Chris Morris, Daniel Kouřil, 2019, Journal of structural biology: X.

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

R. Medema, R. Joosten, A. Perrakis, 2017, The Journal of Biological Chemistry.

Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin

I. Vetter, A. Musacchio, A. Carter, 2022, The Journal of cell biology.

Crystal structure of the E. coli DNA mismatch repair protein MutS in complex with a GT mismatch

M. Lamers, H. Winterwerp, T. Sixma, 2000 .

Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators.

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Distant sequence regions of JBP1 contribute to J-DNA binding

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Current state of automated crystallographic data analysis

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

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Refinement of 2‐Amino‐6‐(4‐methyl‐1‐piperazinyl)‐4‐(tricyclo[3.3.1.13,7]dec‐1‐yl)‐1,3,5‐triazine at Three Different Temperatures using Image‐Plate Data

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Quantitative LC-MS/MS analysis of 5-hydroxymethyl-2'-deoxyuridine to monitor the biological activity of J-binding protein.

H. Rosing, J. Beijnen, A. Perrakis, 2020, Analytical biochemistry.

Interactions between N-Terminal Modules in MPS1 Enable Spindle Checkpoint Silencing

G. Kops, A. Perrakis, Yoshitaka Hiruma, 2018, bioRxiv.

A de novo Designed Possible 5‐Lipoxygenase Inhibitor: α‐Acetoxy‐N‐[1‐(1‐tricyclo[3.3.1.13,7]dec‐1‐yl)ethyl]benzeneacetamide

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The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.

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Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling

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Autotaxin: structure-function and signaling

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SPINE high-throughput crystallization, crystal imaging and recognition techniques: current state, performance analysis, new technologies and future aspects.

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PLA2G16 represents a switch between entry and clearance of Picornaviridae

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Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery.

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