Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
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Title
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
Authors
Keywords
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Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 17, Issue 2, Pages 144
Publisher
MDPI AG
Online
2016-01-26
DOI
10.3390/ijms17020144
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- (2015) Ákos Tarcsay et al. DRUG DISCOVERY TODAY
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- (2014) Hemant Kumar et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- (2014) HuiMin Li et al. Science China-Life Sciences
- A fundamental view of enthalpy–entropy compensation
- (2014) Ulf Ryde MedChemComm
- Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
- (2013) John D. Chodera et al. Annual Review of Biophysics
- Isothermal titration calorimetry of membrane proteins — Progress and challenges
- (2013) Krishna Rajarathnam et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
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- (2013) Simon G. Patching BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- Multiple conformational selection and induced fit events take place in allosteric propagation
- (2013) Ruth Nussinov et al. BIOPHYSICAL CHEMISTRY
- Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
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- 154 Protein folding and binding funnels: a common driving force and a common mechanism
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- 153 Wonderful roles of the entropy in protein dynamics, binding and folding
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- Shaping colloids for self-assembly
- (2013) Stefano Sacanna et al. Nature Communications
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- (2012) Austin D. Vogt et al. BIOCHEMISTRY
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- (2012) P. L. Kastritis et al. Journal of the Royal Society Interface
- Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
- (2012) A. T. Fenley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- Mechanisms of Protein-Ligand Association and Its Modulation by Protein Mutations
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- Free energy calculations of protein–ligand interactions
- (2011) Anita de Ruiter et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Alchemical free energy methods for drug discovery: progress and challenges
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- (2011) Jean-François St-Pierre et al. Journal of Chemical Theory and Computation
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- (2011) Tjelvar S. G. Olsson et al. PROTEIN SCIENCE
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- Basic ingredients of free energy calculations: A review
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- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
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- (2009) Alexey Aleksandrov et al. JOURNAL OF MOLECULAR RECOGNITION
- Assessment of Nonequilibrium Free Energy Methods
- (2009) Benjamin P. Cossins et al. JOURNAL OF PHYSICAL CHEMISTRY B
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- (2009) Yuqing Deng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- 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
- Ligand binding to proteins: The binding landscape model
- (2009) David W. Miller et al. PROTEIN SCIENCE
- Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules
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- Flexible ligand docking to multiple receptor conformations: a practical alternative
- (2008) Maxim Totrov et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry
- (2008) Kawthar Bouchemal DRUG DISCOVERY TODAY
- Entropy driven key-lock assembly
- (2008) G. Odriozola et al. JOURNAL OF CHEMICAL PHYSICS
- Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches
- (2008) Jakob Schluttig et al. JOURNAL OF CHEMICAL PHYSICS
- Adaptive biasing force method for scalar and vector free energy calculations
- (2008) Eric Darve et al. JOURNAL OF CHEMICAL PHYSICS
- Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration
- (2008) Mikolai Fajer et al. Journal of Chemical Theory and Computation
- Protein−Ligand Binding Affinity by Nonequilibrium Free Energy Methods
- (2008) Benjamin P. Cossins et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Polyelectrolyte Adsorption on a Charged Surface. Free Energy Calculation from Monte Carlo Simulations Using Jarzynski Equality
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- (2008) Christoph Hartmann et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
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- Microcalorimetry: a response to challenges in modern biotechnology
- (2008) Tino Krell Microbial Biotechnology
- Strategies and tactics for optimizing the Hit-to-Lead process and beyond—A computational chemistry perspective
- (2007) C MANLY et al. DRUG DISCOVERY TODAY
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