Protein Flexibility in Drug Discovery: From Theory to Computation

Implicit solvent methods for free energy estimation

(2015) Sergio Decherchi et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Molecular mechanics and dynamics: numerical tools to sample the configuration space

(2014) Matteo Masetti   Frontiers in Bioscience-Landmark

Exploring the role of receptor flexibility in structure-based drug discovery

(2013) Ferran Feixas et al.   BIOPHYSICAL CHEMISTRY

Essential role of conformational selection in ligand binding

(2013) Austin D. Vogt et al.   BIOPHYSICAL CHEMISTRY

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites

(2013) Matthew T. Honaker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Collecting and Assessing Human Lactate Dehydrogenase-A Conformations for Structure-Based Virtual Screening

(2013) Rosa Buonfiglio et al.   Journal of Chemical Information and Modeling

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

(2012) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

Modulation of a Pre-existing Conformational Equilibrium Tunes Adenylate Kinase Activity

(2012) Jörgen Ådén et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

(2012) Cho Yeow Koh et al.   STRUCTURE

Essential dynamics: foundation and applications

(2012) Isabella Daidone et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

(2011) Markus A. Lill   BIOCHEMISTRY

Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling

(2011) Mengang Xu et al.   Journal of Chemical Information and Modeling

Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking

(2011) Mengang Xu et al.   Journal of Chemical Information and Modeling

Synergistic folding of two intrinsically disordered proteins: searching for conformational selection

(2011) Debabani Ganguly et al.   Molecular BioSystems

Large conformational changes in proteins: signaling and other functions

(2010) Barry J Grant et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Folding and binding cascades: Dynamic landscapes and population shifts

(2010) Sandeep Kumar et al.   PROTEIN SCIENCE

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

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

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

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

(2009) Roger S. Armen et al.   Journal of Chemical Theory and Computation

The role of dynamic conformational ensembles in biomolecular recognition

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

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

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

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

(2008) William L. Jorgensen et al.   Journal of Chemical Theory and Computation

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY

RosettaLigand Docking with Full Ligand and Receptor Flexibility

(2008) Ian W. Davis et al.   JOURNAL OF MOLECULAR BIOLOGY

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking

(2008) Erin S. D. Bolstad et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS