4.2 Article

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Exploiting tertiary structure through local folds for crystallographic phasing

Massimo Sammito et al.

NATURE METHODS (2013)

Meeting Abstract Chemistry, Multidisciplinary

The Nautilus software for automated nucleic acid model building, Bergen, 7-11 August 2012

Kevin Cowtan

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2012)

Article Biochemical Research Methods

Practical structure solution with ARCIMBOLDO

Dayte Rodriguez et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2012)

Article Biochemistry & Molecular Biology

Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

Lagnajeet Pradhan et al.

BIOCHEMISTRY (2012)

Article Chemistry, Multidisciplinary

Geometric properties of nucleic acids with potential for autobuilding

Tim Gruene et al.

ACTA CRYSTALLOGRAPHICA SECTION A (2011)

Article Biochemistry & Molecular Biology

Crystal structure of the Cys2His2-type zinc finger domain of human DPF2

Wei Zhang et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2011)

Article Biochemistry & Molecular Biology

The structure of the Klf4 DNA-binding domain links to self-renewal and macrophage differentiation

Anja Schuetz et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2011)

Article Biochemistry & Molecular Biology

Nucleosome structural studies

Song Tan et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Structural and Thermodynamic Signatures of DNA Recognition by Mycobacterium tuberculosis DnaA

Oleg V. Tsodikov et al.

JOURNAL OF MOLECULAR BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification

Barry L. Stoddard

STRUCTURE (2011)

Article Biochemical Research Methods

Experimental phasing with SHELXC/D/E: combining chain tracing with density modification

George M. Sheldrick

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

The interaction of four-way DNA junctions with resolving enzymes

David M. J. Lilley

BIOCHEMICAL SOCIETY TRANSACTIONS (2010)

Article Biochemistry & Molecular Biology

Solution Structure of Gfi-1 Zinc Domain Bound to Consensus DNA

Soojin Lee et al.

JOURNAL OF MOLECULAR BIOLOGY (2010)

Article Multidisciplinary Sciences

Structure of the LexA-DNA complex and implications for SOS box measurement

Adrianna P. P. Zhang et al.

NATURE (2010)

Review Biochemical Research Methods

Solving novel RNA structures using only secondary structural fragments

Michael P. Robertson et al.

METHODS (2010)

Article Biochemistry & Molecular Biology

Dali server: conservation mapping in 3D

Liisa Holm et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1)

Ashwini Mishra et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

Characterization and Structure of the Manganese-Responsive Transcriptional Regulator ScaR

Kate E. Stoll et al.

BIOCHEMISTRY (2009)

Article Biochemical Research Methods

Crystallographic ab initio protein structure solution below atomic resolution

Dayte D. Rodriguez et al.

NATURE METHODS (2009)

Article Biochemistry & Molecular Biology

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZADAR1

Sung Chul Ha et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

Interactions between the archaeal transcription repressor FL11 and its coregulators lysine and arginine

Mitsugu Yamada et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

Article Biochemical Research Methods

Building of RNA and DNA double helices into electron density

Frantisek Pavelcik et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2008)

Article Biochemical Research Methods

Pattern-recognition-based detection of planar objects in three-dimensional electron-density maps

Johan Hattne et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2008)

Article Biochemical Research Methods

A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives

Michael P. Robertson et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2008)

Article Chemistry, Multidisciplinary

A short history of SHELX

George M. Sheldrick

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES (2008)

Article Biochemical Research Methods

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

Thomas C. Terwilliger et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2008)

Article Biochemistry & Molecular Biology

Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv

Tripti Shrivastava et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

NAD kinases use substrate-assisted catalysis for specific recognition of NAD

Guillaume Poncet-Montange et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA

Raphael Stoll et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemical Research Methods

Structure determination of the O-methyltransferase NovP using the 'free lunch algorithm' as implemented in SHELXE

Isabel Uson et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2007)

Article Chemistry, Multidisciplinary

Phaser crystallographic software

Airlie J. McCoy et al.

JOURNAL OF APPLIED CRYSTALLOGRAPHY (2007)

Article Biochemistry & Molecular Biology

The structure and transcriptional analysis of a global regulator from Neisseria meningitidis

Jingshan Ren et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2007)

Article Biochemistry & Molecular Biology

Invariance of the zinc finger module: A comparison of the free structure with those in nucleic-acid complexes

Duo Lu et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Structural basis for induced fit mechanisms in DNA recognition by the Pdx1 homeodomain

Antonella Longo et al.

BIOCHEMISTRY (2007)

Article Biochemistry & Molecular Biology

The conformations of the manganese transport regulator of Bacillus subtilis in its metal-free state

Mark A. DeWitt et al.

JOURNAL OF MOLECULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis

Goragot Wisedchaisri et al.

BIOCHEMISTRY (2007)

Article Biochemistry & Molecular Biology

DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6

Daisuke Iyaguchi et al.

STRUCTURE (2007)

Article Biochemistry & Molecular Biology

Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA

David J. Segal et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Review Biochemical Research Methods

ACORN:: a review

J. -X. Yao et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2006)

Article Biology

Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery

TL Blundell et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2006)

Article Biochemistry & Molecular Biology

Induced fit and lock and key recognition of 5 S RNA by zinc fingers of transcription factor IIIA

BM Lee et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

Structural basis of lytic cycle activation by the Epstein-Barr virus ZEBRA protein

C Petosa et al.

MOLECULAR CELL (2006)

Article Biochemistry & Molecular Biology

Autophosphorylation of Archaeoglobus fulgidus Rio2 and crystal structures of its nucleotide-metal ion complexes

N LaRonde-LeBlanc et al.

FEBS JOURNAL (2005)

Article Biochemical Research Methods

Phasing at resolution higher than the experimental resolution

R Caliandro et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Crystal structure of A-fulgidus Rio2 defines a new family of serine protein kinases

N LaRonde-LeBlanc et al.

STRUCTURE (2004)

Letter Biochemistry & Molecular Biology

Announcing the worldwide Protein Data Bank

H Berman et al.

NATURE STRUCTURAL BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Structure of a designed dimeric zinc finger protein bound to DNA

SA Wolfe et al.

BIOCHEMISTRY (2003)

Article Biochemistry & Molecular Biology

Constraints for zinc finger linker design as inferred from X-ray crystal structure of tandem Zif268-DNA complexes

E Peisach et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor

RY Wu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2003)

Review Biochemistry & Molecular Biology

Prokaryotic transcription regulators: more than just the helix-turn-helix motif

JL Huffman et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Mechanism of c-Myb-C/EBPβ cooperation from separated sites on a promoter

TH Tahirov et al.

Article Biochemistry & Molecular Biology

Rearrangement of side-chains in a zif268 mutant highlights the complexities of zinc finger-DNA recognition

JC Miller et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Beyond the recognition code:: Structures of two Cys2His2 zinc finger/TATA box complexes

SA Wolfe et al.

STRUCTURE (2001)

Article Biochemistry & Molecular Biology

Selected peptide extension contacts hydrophobic patch on neighboring zinc finger and mediates dimerization on DNA

BS Wang et al.

NATURE STRUCTURAL BIOLOGY (2001)