List of works - Anastassis Perrakis

"Conditional Restraints": Restraining the Free Atoms in ARP/wARP.

scientific article

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

scientific article

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

scientific article published on 22 April 2020

A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop

scientific article published on 08 January 2019

A knowledge-driven approach for crystallographic protein model completion

scientific article published on 19 March 2008

A new generation of crystallographic validation tools for the protein data bank

scientific article

ARP/wARP and automatic interpretation of protein electron density maps

scientific article (publication date: 2003)

ARP/wARP and molecular replacement

scientific article (publication date: October 2001)

ARP/wARP and molecular replacement: the next generation

scientific article published on 05 December 2007

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

article

ARP/wARP– automated model building and refinement

article

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP ⬇️

scientific article published on January 1, 1998

AlphaFill: enriching AlphaFold models with ligands and cofactors

scientific article published in 2022

Apotheosis, not apocalypse: methods in protein crystallography

scientific article published on 01 November 2000

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

scientific article published on January 2008

Assessment of automatic ligand building in ARP/wARP.

scientific article

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

scientific article (publication date: 2008)

Automated protein model building combined with iterative structure refinement

scientific article (publication date: May 1999)

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

scientific article

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

Autotaxin: structure-function and signaling

scientific article

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

scientific article

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

scientific article

Breaking good resolutions with ARP/wARP.

scientific article published on 28 November 2003

Building and rebuilding N-glycans in protein structure models

scientific article published on 04 April 2019

CCD2: design constructs for protein expression, the easy way

scientific article published on 29 July 2021

CELL DIVISION CYCLE. Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling

scientific article published on 11 June 2015

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

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

scientific article

Cdt1 and geminin in DNA replication initiation

scientific article published on January 2012

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

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

Class I major histocompatibility complexes loaded by a periodate trigger

scientific article

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

scientific article published on 19 September 2006

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

scientific article

Crystal structure of a bacterial chitinase at 2.3 A resolution

scientific article

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

scientific article

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system

scientific article

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

scientific article (publication date: 4 March 2003)

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

scientific article published on October 1997

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

scientific article

Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP

scientific article published on 01 July 2019

Current state of automated crystallographic data analysis.

scientific article

Data Mining of Macromolecular Structures

scientific article

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

scientific article

Developments in the CCP4 molecular-graphics project

scientific article (publication date: December 2004)

Direct binding of Cdt2 to PCNA is important for targeting the CRL4 E3 ligase activity to Cdt1

scientific article published on 31 December 2018

Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis

scientific article published on 18 June 2018

Editorial overview: New constructs and expression of proteins

scientific article published on 9 August 2016

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

scientific article published on 29 March 2011

Eukaryotic expression: developments for structural proteomics.

scientific article published on 19 September 2006

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

scientific article

Evolutionary divergence and conservation of trypsin

scientific article published on 01 January 1994

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

scientific article published on 5 March 2011

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

scientific article published on 19 September 2006

From SPINE to SPINE-2 complexes and beyond ⬇️

scientific article published on May 17, 2011

Getting a macromolecular model: model building, refinement, and validation

article

Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania

scientific article

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

scientific article published on 21 September 2016

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

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

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

scientific article published on 23 November 2017

Homology-based loop modeling yields more complete crystallographic protein structures

article by Bart van Beusekom et al published 1 September 2018 in IUCrJ

Homology-based loop modelling yields more complete crystallographic protein structures

Idas, a novel phylogenetically conserved geminin-related protein, binds to geminin and is required for cell cycle progression

scientific article

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

scientific article published on 19 September 2006

Inhibition of autotaxin by lysophosphatidic acid and sphingosine 1-phosphate

scientific article (publication date: 3 June 2005)

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

scientific article published on 14 September 2011

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

scientific article published in March 2009

Interactions between N-terminal modules in MPS1 enable spindle checkpoint silencing

Investigating a macromolecular complex: the toolkit of methods

scientific article published on 18 May 2011

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

scientific article published on 01 January 2021

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

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

scientific article published in Journal of Biological Chemistry

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

scientific article

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

scientific article

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 beta4 integrin

scientific article

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

article published in 1993

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.

scientific article

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

scientific article

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

scientific article published on 29 August 2017

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

scientific article published in 2021

PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs.

scientific article published in April 1995

PDB_REDO: constructive validation, more than just looking for errors

scientific article published on 16 March 2012

PLA2G16 represents a switch between entry and clearance of Picornaviridae

scientific journal article

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

scientific article

Polo-like kinase-1 controls proteasome-dependent degradation of Claspin during checkpoint recovery

scientific article

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

scientific article published in Journal of Biological Chemistry

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

scientific article published on 01 October 1999

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

scientific article published on 24 April 2009

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

scientific article (publication date: July 2002)

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

scientific article

RNA-binding protein Dnd1 inhibits microRNA access to target mRNA

scientific article

Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators

scientific article

Recombinant cloning strategies for protein expression.

scientific article

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

scientific article

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

scientific article published on 19 September 2006

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

scientific article published on 19 September 2006

Selectivity and Promiscuity in Eph Receptors

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

scientific article published on 10 February 2020

Small is beautiful: protein micro-crystallography

scientific article published in August 1998

Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling

scientific article

Structural basis for Ca2+ regulation in the Na+/Ca2+ exchanger

scientific article published on 8 March 2007

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

scientific article

Structural basis of substrate discrimination and integrin binding by autotaxin

scientific article

Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin

scientific article

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

scientific article

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

scientific article published on 01 January 2001

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

scientific article

Structure of a cephalosporin synthase

scientific article

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

scientific article

Structure of human CLIC3 at 2 A resolution

scientific article

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

scientific article

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

scientific article

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

scientific article published on 01 October 1996

Structure-based design of novel boronic acid-based inhibitors of autotaxin

scientific article published on 9 June 2011

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

scientific article published on 28 September 2012

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

scientific article

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

scientific article published in 1997

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

scientific article published in September 2010

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

scientific article

The CCP4 suite: integrative software for macromolecular crystallography

scientific article published in 2023

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

scientific article

The PDB_REDO server for macromolecular structure model optimization

scientific article

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

scientific article published on 16 October 2019

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 10 July 2019

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

scientific article

The polybasic insertion in autotaxin α confers specific binding to heparin and cell surface heparan sulfate proteoglycans

scientific article published on 13 November 2012

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

scientific article published on 27 March 2007

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

scientific article

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

scientific article published on 31 October 2015

The vertebrate mitotic checkpoint protein BUBR1 is an unusual pseudokinase.

scientific article published in June 2012

Timely deposition of macromolecular structures is necessary for peer review

scientific article

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

scientific article (publication date: December 2004)

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

scientific article published on 28 September 2005

Tryptophan depletion results in tryptophan-to-phenylalanine substitutants

scientific article published on 09 March 2022

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

scientific article published on 16 July 2021

UV-induced ligand exchange in MHC class I protein crystals

scientific article

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

scientific article

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

scientific article

Vasohibins encode tubulin detyrosinating activity

scientific article

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

scientific article (publication date: July 1997)

List of works by Anastassis Perrakis

"Conditional Restraints": Restraining the Free Atoms in ARP/wARP.

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

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

A crystal structure of the human protein kinase Mps1 reveals an ordered conformation of the activation loop

A knowledge-driven approach for crystallographic protein model completion

A new generation of crystallographic validation tools for the protein data bank

ARP/wARP and automatic interpretation of protein electron density maps

ARP/wARP and molecular replacement

ARP/wARP and molecular replacement: the next generation

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

ARP/wARP– automated model building and refinement

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP ⬇️

AlphaFill: enriching AlphaFold models with ligands and cofactors

Apotheosis, not apocalypse: methods in protein crystallography

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

Assessment of automatic ligand building in ARP/wARP.

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

Automated protein model building combined with iterative structure refinement

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

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

Autotaxin: structure-function and signaling

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

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

Breaking good resolutions with ARP/wARP.

Building and rebuilding N-glycans in protein structure models

CCD<sup>2</sup>: design constructs for protein expression, the easy way

CELL DIVISION CYCLE. Competition between MPS1 and microtubules at kinetochores regulates spindle checkpoint signaling

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

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

Cdt1 and geminin in DNA replication initiation

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

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

Class I major histocompatibility complexes loaded by a periodate trigger

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

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

Crystal structure of a bacterial chitinase at 2.3 A resolution

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

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system

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

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

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

Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP

Current state of automated crystallographic data analysis.

Data Mining of Macromolecular Structures

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

Developments in the CCP4 molecular-graphics project

Direct binding of Cdt2 to PCNA is important for targeting the CRL4 E3 ligase activity to Cdt1

Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis

Editorial overview: New constructs and expression of proteins

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

Eukaryotic expression: developments for structural proteomics.

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

Evolutionary divergence and conservation of trypsin

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

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

From SPINE to SPINE-2 complexes and beyond ⬇️

Getting a macromolecular model: model building, refinement, and validation

Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania

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

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

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

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

Homology-based loop modeling yields more complete crystallographic protein structures

Homology-based loop modelling yields more complete crystallographic protein structures

Idas, a novel phylogenetically conserved geminin-related protein, binds to geminin and is required for cell cycle progression

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

Inhibition of autotaxin by lysophosphatidic acid and sphingosine 1-phosphate

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

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

Interactions between N-terminal modules in MPS1 enable spindle checkpoint silencing

Investigating a macromolecular complex: the toolkit of methods

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

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

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

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

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

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 beta4 integrin

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

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.