A flexible docking scheme to explore the binding selectivity of PDZ domains

No abstract is available for this paper.

• Publication year

  2010

• Venue

  Protein Science

• Publication date

  2010-05-01

• Fields of study

  Medicine, Chemistry

• Identifiers
  DOI 10.1002/pro.366PMID 20196074PMCID PMC2868235
• 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.

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

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• Optimizing Dvl PDZ domain inhibitor by exploring chemical space

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• Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics

  2009cited by this paper
• A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X‐ray, and computations

  2009cited by this paper
• RosettaLigand docking with full ligand and receptor flexibility.

  2009influential reference
• Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

  2009influential reference
• Hidden dynamic allostery in a PDZ domain

  2009cited by this paper
• Sending Signals Dynamically

  2009cited by this paper
• Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.

  2009cited by this paper
• The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

  2009cited by this paper
• Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking

  2008cited by this paper
• Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein.

  2008cited by this paper
• Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking.

  2008cited by this paper
• Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking

  2008cited by this paper
• Target flexibility: an emerging consideration in drug discovery and design.

  2008cited by this paper
• Structural flexibility in proteins: impact of the crystal environment

  2008cited by this paper
• Rescoring docking hit lists for model cavity sites: predictions and experimental testing.

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• MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

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• Flexible ligand docking to multiple receptor conformations: a practical alternative.

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• Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.

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• Exploring experimental sources of multiple protein conformations in structure-based drug design.

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• FireDock: Fast interaction refinement in molecular docking

  2007cited by this paper
• Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

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• Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

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• PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome

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• The Gambler’s and Hot-Hand Fallacies: Theory and Applications

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• Automatic prediction of protein interactions with large scale motion

  2007cited by this paper
• The PDZ Domain as a Complex Adaptive System

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• vGNM: a better model for understanding the dynamics of proteins in crystals.

  2007cited by this paper
• Pump‐probe molecular dynamics as a tool for studying protein motion and long range coupling

  2006cited by this paper
• Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

  2006cited by this paper
• Statistical potential for assessment and prediction of protein structures

  2006cited by this paper
• ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

  2006influential reference
• Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study.

  2006cited by this paper
• Protein–ligand docking: Current status and future challenges

  2006cited by this paper
• Docking of photosystem I subunit C using a constrained geometric simulation.

  2006cited by this paper
• Docking: successes and challenges.

  2005cited by this paper
• Molecular docking of balanol to dynamics snapshots of protein kinase A

  2005cited by this paper
• The Gaussian Network Model: Theory and Applications

  2005cited by this paper
• Representing receptor flexibility in ligand docking through relevant normal modes.

  2005cited by this paper
• Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking

  2005cited by this paper
• Molecular Determinants for the Complex Binding Specificity of the PDZ Domain in PICK1*

  2005cited by this paper
• Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state.

  2005cited by this paper
• Functional Plasticity in the Substrate Binding Site of β-Secretase

  2005cited by this paper
• Docking essential dynamics eigenstructures

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• DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.

  2005cited by this paper
• A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains.

  2005influential reference
• Accounting for global protein deformability during protein-protein and protein-ligand docking.

  2005cited by this paper
• Functional plasticity in the substrate binding site of beta-secretase.

  2005cited by this paper
• Refinement of docked protein–ligand and protein–DNA structures using low frequency normal mode amplitude optimization

  2005cited by this paper
• Normal-modes-based prediction of protein conformational changes guided by distance constraints.

  2005cited by this paper
• Functional dynamics of PDZ binding domains: a normal-mode analysis.

  2005cited by this paper
• Normal mode analysis : theory and applications to biological and chemical systems

  2005cited by this paper
• Unveiling the full potential of flexible receptor docking using multiple crystallographic structures.

  2005cited by this paper
• Assessing scoring functions for protein-ligand interactions.

  2004cited by this paper
• Predictions of protein flexibility: First‐order measures

  2004cited by this paper
• Ligand-dependent dynamics and intramolecular signaling in a PDZ domain.

  2004cited by this paper
• The PDZ Domain of PICK1 Differentially Accepts Protein Kinase C-α and GluR2 as Interacting Ligands*

  2004cited by this paper
• Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP

  2004cited by this paper
• Protein flexibility and computer-aided drug design.

  2003cited by this paper
• 3D-Jury: A Simple Approach to Improve Protein Structure Predictions

  2003cited by this paper
• Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.

  2003cited by this paper
• Comparative evaluation of 11 scoring functions for molecular docking.

  2003cited by this paper
• Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.

  2003cited by this paper
• Novel Mode of Ligand Recognition by the Erbin PDZ Domain*

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• Principles of docking: An overview of search algorithms and a guide to scoring functions

  2002cited by this paper
• ESyPred 3 D : Prediction of proteins 3 D structures

  2002cited by this paper
• ESyPred3D: Prediction of proteins 3D structures

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• Further development and validation of empirical scoring functions for structure-based binding affinity prediction

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• The Erbin PDZ Domain Binds with High Affinity and Specificity to the Carboxyl Termini of δ-Catenin and ARVCF*

  2002cited by this paper
• Computational drug design accommodating receptor flexibility: the relaxed complex scheme.

  2002cited by this paper
• Structure prediction meta server

  2001cited by this paper
• Conformational change of proteins arising from normal mode calculations.

  2001cited by this paper
• Anisotropy of fluctuation dynamics of proteins with an elastic network model.

  2001influential reference
• A single glycine residue at the entrance to the first membrane-spanning domain of the gamma-aminobutyric acid type A receptor beta(2) subunit affects allosteric sensitivity to GABA and anesthetics.

  2000cited by this paper
• Knowledge-based scoring function to predict protein-ligand interactions.

  2000cited by this paper
• Accommodating protein flexibility in computational drug design.

  2000cited by this paper
• The Protein Data Bank

  2000cited by this paper
• Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model

  2000cited by this paper
• Exploring the dynamic information content of a protein NMR structure: Comparison of a molecular dynamics simulation with the NMR and X‐ray structures of Escherichia coli ribonuclease HI

  1999cited by this paper
• Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

  1999cited by this paper
• Replica-exchange molecular dynamics method for protein folding

  1999cited by this paper
• Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

  1998cited by this paper
• SMART, a simple modular architecture research tool: identification of signaling domains.

  1998cited by this paper
• Recognition of Unique Carboxyl-Terminal Motifs by Distinct PDZ Domains

  1997cited by this paper
• Specific Interaction of the PDZ Domain Protein PICK1 with the COOH Terminus of Protein Kinase C-α*

  1997cited by this paper
• Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

  1997cited by this paper
• Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation

  1997cited by this paper
• The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

  1997cited by this paper
• PDZ domain proteins: scaffolds for signaling complexes.

  1997cited by this paper
• SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling

  1997cited by this paper
• Molecular modelling: Principles and applications

  1997cited by this paper
• Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis.

  1996cited by this paper
• Comparative protein modelling by satisfaction of spatial restraints.

  1993cited by this paper
• Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications

  1989cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper

• Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.

  2026cites this paper
• Viral subversion of the cell polarity regulator Scribble

  2023cites this paper
• Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity

  2021cites this paper
• Specificity in PDZ-peptide interaction networks: Computational analysis and review

  2020cites this paper
• Substitutions at Nonconserved Rheostat Positions Modulate Function by Rewiring Long-Range, Dynamic Interactions

  2020cites this paper
• The electrostatic allostery could be the trigger for the changes in dynamics for the PDZ domain of PICK1

  2020cites this paper
• Substitutions at Non-Conserved Rheostat Positions Modulate Function by Re-Wiring Long-Range, Dynamic Interactions

  2020cites this paper
• The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution.

  2020cites this paper
• Multiscale weighted colored graphs for protein flexibility and rigidity analysis.

  2018cites this paper
• Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling

  2018cites this paper
• Ancient Thioredoxins Evolved to Modern Day Stability-Function Requirement by Altering Native State Ensemble

  2018cites this paper
• Resurrected Ancestral Proteins as Scaffolds for Protein Engineering

  2017cites this paper
• A review of geometric, topological and graph theory apparatuses for the modeling and analysis of biomolecular data

  2016cites this paper
• Structural and functional consequences of single mutations at the high affinity binding site of cyanovirin-N

  2016cites this paper
• Incorporation of side chain flexibility into protein binding pockets using MTflex.

  2016cites this paper
• Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

  2016cites this paper
• A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs.

  2015cites this paper
• Flexibility–rigidity index for protein–nucleic acid flexibility and fluctuation analysis

  2015cites this paper
• Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme.

  2015cites this paper
• On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein.

  2015cites this paper
• Exploring Multiple Binding Modes Using Confined Replica Exchange Molecular Dynamics.

  2015cites this paper
• Modeling Protein Ligand Interactions Using Multi-Scale Computational Approaches

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• Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).

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• A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding.

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• Ensemble-Based Docking Using Biased Molecular Dynamics

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• Elastic network models capture the motions apparent within ensembles of RNA structures

  2014cites this paper
• Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis.

  2014cites this paper
• BP-Dock: A Flexible Docking Scheme for Exploring Protein-Ligand Interactions Based on Unbound Structures

  2014cites this paper
• Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

  2014cites this paper
• Structural Basis Of Epigenetic Regulation And Protein Scaffolding In Development And Diseases

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• Glycan-Cyanovirin-N Interactions and Designed WW Domains: Combining Experimental and Computational Studies

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• New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping

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• Artificial neural networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry.

  2013cites this paper
• The antiviral lectin cyanovirin-N: probing multivalency and glycan recognition through experimental and computational approaches.

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• Modeling peptide-protein interactions.

  2012cites this paper
• From laptop to benchtop to bedside: structure-based drug design on protein targets.

  2012cites this paper
• The binding affinities of proteins interacting with the PDZ domain of PICK1

  2012cites this paper
• The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains

  2012cites this paper
• Normal mode-based approaches in receptor ensemble docking.

  2012cites this paper
• Reduced False Positives in PDZ Binding Prediction Using Sequence and Structural Descriptors

  2012cites this paper
• Towards a better understanding of protein interaction specificities in cell signalling - PDZ domains in the spotlight of computational and experimental approaches

  2012cites this paper
• Hybrid approaches to molecular simulation.

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• The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains

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• Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks

  2011cites this paper
• Role of protein flexibility in the discovery of new drugs

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• Structure and dynamics of the MAGUK core of PSD-95

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• Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

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• Novel computational biology methods and their applications to drug discovery

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• Molecular Modeling of Neurokinin B and Tachykinin NK3 Receptor Complex

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• Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

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• Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

  2011cites this paper
• Multiple‐Targeting and Conformational Selection in the Estrogen Receptor: Computation and Experiment

  2011cites this paper
• Interaction prediction and classification of PDZ domains

  2010cites this paper
• Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E.

  2010cites this paper
• On the functional significance of soft modes predicted by coarse-grained models for membrane proteins

  2010cites this paper
• Manipulation of conformational change in proteins by single-residue perturbations.

  2010cites this paper