Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems

Structural heterogeneity and dynamics in protein evolution and design

(2018) Kristoffer E Johansson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

(2017) Fei Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418)

(2017) A. Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational selection or induced fit? New insights from old principles

(2016) Denis Michel   BIOCHIMIE

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution

(2016) Zeynep Kurkcuoglu et al.   Journal of Chemical Theory and Computation

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

(2016) Zeynep Kurkcuoglu et al.   PLoS One

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1

(2016) A. Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pushing the Backbone in Protein-Protein Docking

(2016) Daisuke Kuroda et al.   STRUCTURE

Data publication with the structural biology data grid supports live analysis

(2016) Peter A. Meyer et al.   Nature Communications

Adaptability of protein structures to enable functional interactions and evolutionary implications

(2015) Turkan Haliloglu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Integrative computational modeling of protein interactions

(2014) João P. G. L. M. Rodrigues et al.   FEBS Journal

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

Corrigendum to “Structural Comparison of Fucosylated and Nonfucosylated Fc Fragments of Human Immunoglobulin G1” [J. Mol. Biol. 386/3 (2007) 767–779]

(2011) Shigeki Matsumiya et al.   JOURNAL OF MOLECULAR BIOLOGY

A Multidomain Flexible Docking Approach to Deal with Large Conformational Changes in the Modeling of Biomolecular Complexes

(2011) Ezgi Karaca et al.   STRUCTURE

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

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

(2010) Marc van Dijk et al.   NUCLEIC ACIDS RESEARCH

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model

(2009) Ozge Kurkcuoglu et al.   BIOPHYSICAL JOURNAL

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Crystal structure of reduced thioredoxin reductase from Escherichia coli: Structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor

(2009) Brett W. Lennon et al.   PROTEIN SCIENCE

The NMR Structure and Dynamics of the Two-Domain Tick Carboxypeptidase Inhibitor Reveal Flexibility in Its Free Form and Stiffness upon Binding to Human Carboxypeptidase B†‡

(2008) David Pantoja-Uceda et al.   BIOCHEMISTRY