4.3 Article

Solvated protein-DNA docking using HADDOCK

Related references

Note: Only part of the references are listed.
Review Chemistry, Multidisciplinary

Frontiers in Molecular Dynamics Simulations of DNA

Alberto Perez et al.

ACCOUNTS OF CHEMICAL RESEARCH (2012)

Article Biochemical Research Methods

PDB_REDO: constructive validation, more than just looking for errors

Robbie P. Joosten et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2012)

Article Biochemistry & Molecular Biology

Atomistic modeling of protein-DNA interaction specificity: progress and applications

Limin Angela Liu et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2012)

Article Chemistry, Multidisciplinary

Next challenges in protein-protein docking: from proteome to interactome and beyond

Adrien S. J. Melquiond et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2012)

Article Biochemistry & Molecular Biology

Exploring translocation of proteins on DNA by NMR

G. Marius Clore

JOURNAL OF BIOMOLECULAR NMR (2011)

Review Biochemistry & Molecular Biology

The impact of next-generation sequencing on genomics

Jun Zhang et al.

JOURNAL OF GENETICS AND GENOMICS (2011)

Review Biochemical Research Methods

Proteogenomics

Santosh Renuse et al.

PROTEOMICS (2011)

Article Multidisciplinary Sciences

Adhesive water networks facilitate binding of protein interfaces

Mazen Ahmad et al.

NATURE COMMUNICATIONS (2011)

Article Biophysics

Modeling the Hydration Layer around Proteins: HyPred

Jouko J. Virtanen et al.

BIOPHYSICAL JOURNAL (2010)

Article Chemistry, Multidisciplinary

Fast Determination of the Optimal Rotational Matrix for Macromolecular Superpositions

Pu Liu et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

Docking and scoring protein interactions: CAPRI 2009

Marc F. Lensink et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Blind predictions of protein interfaces by docking calculations in CAPRI

Marc F. Lensink et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

3D-DART: a DNA structure modelling server

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Chemistry, Multidisciplinary

Water as an active constituent in cell biology

Philip Ball

CHEMICAL REVIEWS (2008)

Article Biochemistry & Molecular Biology

Structural insight into the mechanisms of Wnt signaling antagonism by Dkk

Lijun Chen et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Chemistry, Multidisciplinary

Energy-based prediction of amino acid-nucleotide base recognition

Anna Marabotti et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Medicinal

Exploiting ordered waters in molecular docking

Niu Huang et al.

JOURNAL OF MEDICINAL CHEMISTRY (2008)

Article Biochemistry & Molecular Biology

A protein-DNA docking benchmark

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

Gene regulation in the postgenomic era: Technology takes the wheel

Rebecca K. Dunn et al.

MOLECULAR CELL (2007)

Article Biochemistry & Molecular Biology

HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

Sjoerd J. De Vries et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Review Biophysics

Energetics of the protein-DNA-water interaction

Francesca Spyrakis et al.

BMC STRUCTURAL BIOLOGY (2007)

Article Biochemical Research Methods

Version 1.2 of the Crystallography and NMR system

Axel T. Brunger

NATURE PROTOCOLS (2007)

Article Biochemistry & Molecular Biology

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Helen Berman et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Chemistry, Physical

Water at biomolecular binding interfaces

Zheng Li et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2007)

Article Biochemical Research Methods

Solvated docking: introducing water into the modelling of biomolecular complexes

Aalt D. J. van Dijk et al.

BIOINFORMATICS (2006)

Review Cell Biology

Structural systems biology: modelling protein interactions

P Aloy et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2006)

Article Chemistry, Medicinal

Docking of Aminoglycosides to hydrated and flexible RNA

N Moitessier et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2006)

Review Biochemistry & Molecular Biology

Interactome: gateway into systems biology

ME Cusick et al.

HUMAN MOLECULAR GENETICS (2005)

Article Chemistry, Multidisciplinary

Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

DL Theobald

ACTA CRYSTALLOGRAPHICA SECTION A (2005)

Article Biochemistry & Molecular Biology

RECOORD:: A recalculated coordinate database of 500+proteins from the PDB using restraints from the BioMagResBank

AJ Nederveen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Review Biochemistry & Molecular Biology

Data-driven docking for the study of biomolecular complexes

ADJ van Dijk et al.

FEBS JOURNAL (2005)

Article Biochemistry & Molecular Biology

Identification of protein-protein interaction sites from docking energy landscapes

J Fernández-Recio et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Multidisciplinary Sciences

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes

CG Kalodimos et al.

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Predicting interactions of winged-helix transcription factors with DNA

VA Roberts et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Multidisciplinary Sciences

A vision for the future of genomics research

FS Collins et al.

NATURE (2003)

Article Chemistry, Multidisciplinary

HADDOCK: A protein-protein docking approach based on biochemical or biophysical information

C Dominguez et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)

Review Chemistry, Multidisciplinary

Solvation and hydration of proteins and mucleic acids: A theoretical view of simulation and experiment

V Makarov et al.

ACCOUNTS OF CHEMICAL RESEARCH (2002)

Review Chemistry, Multidisciplinary

Simulations of nucleic acids and their complexes

E Giudice et al.

ACCOUNTS OF CHEMICAL RESEARCH (2002)

Article Biochemistry & Molecular Biology

Do water molecules mediate protein-DNA recognition?

CK Reddy et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

NM Luscombe et al.

NUCLEIC ACIDS RESEARCH (2001)

Review Multidisciplinary Sciences

Proteomics to study genes and genomes

A Pandey et al.

NATURE (2000)