Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Journal of Chemical Information and Modeling

• Publication date

  2006-04-26

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/ci050412xPMID 16859311
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Comparative virtual and experimental high-throughput screening for glycogen synthase kinase-3beta inhibitors.

  2005cited by this paper
• Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (beta-secretase).

  2005cited by this paper
• Virtual screening for beta-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228.

  2005cited by this paper
• Structural locations and functional roles of new subsites S5, S6, and S7 in memapsin 2 (beta-secretase).

  2005cited by this paper
• Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases.

  2004cited by this paper
• Flap position of free memapsin 2 (beta-secretase), a model for flap opening in aspartic protease catalysis.

  2004cited by this paper
• Apo and inhibitor complex structures of BACE (beta-secretase).

  2004cited by this paper
• Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment

  2004cited by this paper
• The structure of JNK3 in complex with small molecule inhibitors: structural basis for potency and selectivity.

  2003cited by this paper
• Implications of protein flexibility for drug discovery

  2003cited by this paper
• Flexible docking under pharmacophore type constraints

  2002cited by this paper
• Structure-based virtual screening: an overview.

  2002cited by this paper
• Crystal structure of memapsin 2 (beta-secretase) in complex with an inhibitor OM00-3.

  2002cited by this paper
• FlexE: efficient molecular docking considering protein structure variations.

  2001cited by this paper
• Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor.

  2000cited by this paper
• The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

  1999cited by this paper
• Crystal structure of JNK3: a kinase implicated in neuronal apoptosis.

  1998cited by this paper
• Computation of the binding of fully flexible peptides to proteins with flexible side chains

  1997cited by this paper
• A fast flexible docking method using an incremental construction algorithm.

  1996cited by this paper
• Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation.

  1995cited by this paper
• Ligand docking to proteins with discrete side-chain flexibility.

  1994cited by this paper
• "Soft docking": matching of molecular surface cubes.

  1991cited by this paper

• NMR Data‐Driven Docking of HDM2‐Inhibitor Complexes

  2022cites this paper
• EDock‐ML: A web server for using ensemble docking with machine learning to aid drug discovery

  2021cites this paper
• Targeting the C-Terminal Domain Small Phosphatase 1

  2020cites this paper
• Benchmarking Data Sets from PubChem BioAssay Data: Current Scenario and Room for Improvement

  2020cites this paper
• Prospecting for new catechol-O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson’s disease: a study by molecular dynamics and structure-based virtual screening

  2020cites this paper
• Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking

  2018cites this paper
• Drug Design: Principles and Applications

  2017cites this paper
• Applications of Computer-Aided Drug Design

  2017cites this paper
• Alzheimer's disease drug development based on Computer-Aided Drug Design.

  2016cites this paper
• siRNA screen identifies QPCT as a druggable target for Huntington’s disease

  2015cites this paper
• Flexible receptor docking for drug discovery

  2015cites this paper
• A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins

  2015cites this paper
• Tubulin Inhibitor Identification by Bioactive Conformation Alignment Pharmacophore‐Guided Virtual Screening

  2015cites this paper
• Integrated approach to structure-based enzymatic drug design: molecular modeling, spectroscopy, and experimental bioactivity.

  2014cites this paper
• (How to) Profit from Molecular Dynamics-based Ensemble Docking

  2014cites this paper
• Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments

  2014cites this paper
• Structure-based β-secretase (BACE1) inhibitors.

  2014cites this paper
• Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method

  2014cites this paper
• Cognitive Enhancers (Nootropics). Part 2: Drugs Interacting with Enzymes

  2013cites this paper
• Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)

  2012cites this paper
• Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)

  2012cites this paper
• Computational methods in the discovery and design of BACE-1 inhibitors.

  2012cites this paper
• Modeling loop backbone flexibility in receptor‐ligand docking simulations

  2012cites this paper
• Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design

  2012cites this paper
• Flexible protein‐ligand docking using the Fleksy protocol

  2012cites this paper
• Receptor flexibility in small‐molecule docking calculations

  2011cites this paper
• Accurate Prediction of the Bound Form of the Akt Pleckstrin Homology Domain Using Normal Mode Analysis To Explore Structural Flexibility

  2011cites this paper
• Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

  2011cites this paper
• Protein-ligand docking.

  2011cites this paper
• Receptor Flexibility in Ligand Docking and Virtual Screening

  2011cites this paper
• Molecular recognition and drug-lead identification: what can molecular simulations tell us?

  2010cites this paper
• How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

  2010cites this paper
• Structure and modeling in the design of β‐ and γ‐secretase inhibitors

  2009cites this paper
• Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility

  2009cites this paper
• Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

  2009cites this paper
• Scoring Ensembles of Docked Protein: Ligand Interactions for Virtual Lead Optimization

  2009cites this paper
• Docking and scoring with alternative side‐chain conformations

  2009cites this paper
• Flexible ligand docking to multiple receptor conformations: a practical alternative.

  2008cites this paper
• Modeling of flexible side chains for protein-ligand docking

  2008cites this paper
• Essential factors for successful virtual screening.

  2008cites this paper
• Improving database enrichment through ensemble docking

  2008cites this paper
• Small Molecule Docking

  2008cites this paper
• Ensemble‐Docking Approach on BACE‐1: Pharmacophore Perception and Guidelines for Drug Design

  2007cites this paper
• Processing of small molecule databases for automated docking.

  2007cites this paper
• Loopholes and missing links in protein modeling

  2007cites this paper
• Impact of ligand protonation on virtual screening against beta-secretase (BACE1).

  2007cites this paper
• FlexE ensemble docking approach to virtual screening for CDK2 inhibitors

  2007cites this paper
• A flexible approach to induced fit docking.

  2007cites this paper
• Structure-guided design of β-secretase (BACE-1) inhibitors

  2007cites this paper
• Lead optimization via high-throughput molecular docking.

  2007cites this paper
• Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE Against JNK-3 and β-Secretase.

  2006cites this paper
• Pipeline to Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and FLAP. JOURNAL OF CHEMICAL INFORMATION AND MODELLING

  year unknowncites this paper