Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches
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Title
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches
Authors
Keywords
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Journal
Journal of the Royal Society Interface
Volume 9, Issue 66, Pages 20-33
Publisher
The Royal Society
Online
2011-10-13
DOI
10.1098/rsif.2011.0584
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Note: Only part of the references are listed.- On the Origin of the Stronger Binding of PIB over Thioflavin T to Protofibrils of the Alzheimer Amyloid-β Peptide: A Molecular Dynamics Study
- (2011) Chun Wu et al. BIOPHYSICAL JOURNAL
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- (2011) Simon Mitternacht et al. JOURNAL OF MOLECULAR BIOLOGY
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- (2011) Katrin Hochdörffer et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
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- (2011) Yibing Shan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Structure and function of an irreversible agonist-β2 adrenoceptor complex
- (2011) Daniel M. Rosenbaum et al. NATURE
- Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
- (2011) I. Buch et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- PubChem3D: Conformer generation
- (2011) Evan E Bolton et al. Journal of Cheminformatics
- Mapping Conformational Ensembles of Aβ Oligomers in Molecular Dynamics Simulations
- (2010) Seongwon Kim et al. BIOPHYSICAL JOURNAL
- The Role of Water Molecules in Computational Drug Design
- (2010) Stephanie de Beer et al. CURRENT TOPICS IN MEDICINAL CHEMISTRY
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- (2010) Paul C. D. Hawkins et al. Journal of Chemical Information and Modeling
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- (2010) Antonios Samiotakis et al. JOURNAL OF CHEMICAL PHYSICS
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- (2010) Ezgi Karaca et al. MOLECULAR & CELLULAR PROTEOMICS
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- (2010) M. A. Miteva et al. NUCLEIC ACIDS RESEARCH
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- (2010) E. Mashiach et al. NUCLEIC ACIDS RESEARCH
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- (2008) Shantanu Sharma Frontiers in Bioscience-Landmark
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- (2008) Cristiano R. W. Guimarães et al. Journal of Chemical Information and Modeling
- MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening
- (2008) Shuangye Yin et al. Journal of Chemical Information and Modeling
- Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems
- (2008) Esther Kellenberger et al. Journal of Chemical Information and Modeling
- Assessment of programs for ligand binding affinity prediction
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- Identification of Protein Interaction Partners and Protein–Protein Interaction Sites
- (2008) Sophie Sacquin-Mora et al. JOURNAL OF MOLECULAR BIOLOGY
- Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent
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- Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
- (2008) Anna Berteotti et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
- (2008) Nicolas Simonis et al. NATURE METHODS
- The RosettaDock server for local protein-protein docking
- (2008) S. Lyskov et al. NUCLEIC ACIDS RESEARCH
- 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
- C-terminal peptides coassemble into A 42 oligomers and protect neurons against A 42-induced neurotoxicity
- (2008) E. A. Fradinger et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Protein-protein docking by simulating the process of association subject to biochemical constraints
- (2008) Domantas Motiejunas et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protein-protein docking benchmark version 3.0
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- Targeting the early steps of Aβ16-22 protofibril disassembly by N-methylated inhibitors: A numerical study
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