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Receptor flexibility in small‐molecule docking calculations

https://doi.org/10.1002/wcms.29
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long‐time molecular dynamics simulations
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Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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FlexE: efficient molecular docking considering protein structure variations
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Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement 1 1Edited by J. Thornton
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A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
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Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors
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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
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How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding
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Flexible ligand docking to multiple receptor conformations: a practical alternative
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Geometry-Based Sampling of Conformational Transitions in Proteins
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Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of F itted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors
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Ensemble Docking from Homology Models
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Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
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Protein Flexibility and Species Specificity in Structure-Based Drug Discovery: Dihydrofolate Reductase as a Test System
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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
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Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
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Raptor: Combining Dual-Shell Representation, Induced-Fit Simulation, and Hydrophobicity Scoring in Receptor Modeling: Application toward the Simulation of Structurally Diverse Ligand Sets
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Soft Docking and Multiple Receptor Conformations in Virtual Screening
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A Critical Assessment of Docking Programs and Scoring Functions
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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Benchmarking Sets for Molecular Docking
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Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction
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A Flexible Approach to Induced Fit Docking
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Protein−Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking
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Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins
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Intrinsic motions along an enzymatic reaction trajectory
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The role of dynamic conformational ensembles in biomolecular recognition
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Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition
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Relation between native ensembles and experimental structures of proteins
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A consensus view of protein dynamics
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Conformational selection or induced fit: A flux description of reaction mechanism
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Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands
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FlexE ensemble docking approach to virtual screening for CDK2 inhibitors
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Hierarchical and multi-resolution representation of protein flexibility
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DFprot: a webtool for predicting local chain deformability
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Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
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Computation of the binding of fully flexible peptides to proteins with flexible side chains
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Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis
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Improved side‐chain modeling for protein–protein docking
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Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography
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Atomic-Level Characterization of the Structural Dynamics of Proteins
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Calculation of Protein-Ligand Binding Affinities
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Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
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Docking: Successes and Challenges
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Simplified Computational Methods for the Analysis of Protein Flexibility

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.5772/35169openalex-snapshot
Recent Advances and Future Trend on the Emerging Role of GPUs as Platforms for Virtual Screening-Based Drug Discovery
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