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

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

(2015) Zeynep Kurkcuoglu et al.   BIOPHYSICAL JOURNAL

Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State

(2014) Arzu Uyar et al.   BIOPHYSICAL JOURNAL

BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

(2014) Ashini Bolia et al.   Journal of Chemical Information and Modeling

Sampling large conformational transitions: adenylate kinase as a testing ground

(2014) Sean L. Seyler et al.   MOLECULAR SIMULATION

Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase

(2013) Mert Gur et al.   BIOPHYSICAL JOURNAL

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

(2013) Ibrahim Al-Bluwi et al.   BMC STRUCTURAL BIOLOGY

A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex

(2012) E. Demet Akten et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking

(2012) Matthias Dietzen et al.   Journal of Chemical Information and Modeling

Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates

(2012) Yong Wang et al.   Journal of Chemical Theory and Computation

Conformational Sampling of Maltose-Transporter Components in Cartesian Collective Variables Is Governed by the Low-Frequency Normal Modes

(2012) H. Vashisth et al.   Journal of Physical Chemistry Letters

Advances in integrative modeling of biomolecular complexes

(2012) Ezgi Karaca et al.   METHODS

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

(2012) J E Jimenez-Roldan et al.   PHYSICAL BIOLOGY

Protein flexibility in docking and surface mapping

(2012) Katrina W. Lexa et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Predicting protein ligand binding motions with the conformation explorer

(2011) Samuel C Flores et al.   BMC BIOINFORMATICS

A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins

(2011) Aqeel Ahmed et al.   Journal of Chemical Information and Modeling

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking*

(2011) Simon Leis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human

(2011) Zeynep Kurkcuoglu  et al.   Molecular Informatics

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

(2011) Ezgi Karaca et al.   STRUCTURE

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The HADDOCK web server for data-driven biomolecular docking

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

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

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

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

(2010) Daniel Seeliger et al.   PLoS Computational Biology

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

(2009) Ozge Kurkcuoglu et al.   BIOPHYSICAL JOURNAL

Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open↔Closed Transitions

(2009) Oliver Beckstein et al.   JOURNAL OF MOLECULAR BIOLOGY

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

(2009) T. P. Schrank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The energy profiles of atomic conformational transition intermediates of adenylate kinase

(2009) Yaping Feng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

(2009) Canan Atilgan et al.   PLoS Computational Biology

Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

(2008) Nigar Kantarci-Carsibasi et al.   BIOPHYSICAL JOURNAL

Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics

(2008) Francesco Pontiggia et al.   BIOPHYSICAL JOURNAL

Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking

(2008) Andreas May et al.   JOURNAL OF MEDICINAL CHEMISTRY

Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking

(2008) S. E. Dobbins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase

(2008) Igor Mochalkin et al.   PROTEIN SCIENCE