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Rapid Identification of Ligand-Binding Sites by Using an Assignment-Free NMR Approach

https://doi.org/10.1021/jm4014357
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Automated prediction of ligand‐binding sites in proteins
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The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria
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NMR backbone assignment of the mitogen-activated protein (MAP) kinase p38
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Novel trends in high-throughput screening
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Shape Variation in Protein Binding Pockets and their Ligands
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HotPatch: A Statistical A pproach to Finding Biologically Relevant Features on Protein Surfaces
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A Novel Lipid Binding Site Formed by the MAP Kinase Insert in p38α
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p38α MAP Kinase C-Terminal Domain Binding Pocket Characterized by Crystallographic and Computational Analyses
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Lipid Molecules Induce p38α Activation via a Novel Molecular Switch
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Pocket extraction on proteins via the Voronoi diagram of spheres
inferredcites →https://doi.org/10.1016/j.jsb.2007.09.005openalex-snapshot
PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins
inferredcites →https://doi.org/10.1016/j.jsb.2011.04.001openalex-snapshot
Rapid identification of protein–protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements
inferredcites →https://doi.org/10.1016/j.str.2007.09.017openalex-snapshot
Geometry-Based Sampling of Conformational Transitions in Proteins
inferredcites →https://doi.org/10.1016/s0959-440x(02)00284-1openalex-snapshot
Evolutionary predictions of binding surfaces and interactions
inferredcites →https://doi.org/10.1021/ci6002202openalex-snapshot
Use of Amino Acid Composition to Predict Ligand-Binding Sites
inferredcites →https://doi.org/10.1021/ci600229zopenalex-snapshot
Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model
inferredcites →https://doi.org/10.1021/ci700149kopenalex-snapshot
Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces
inferredcites →https://doi.org/10.1021/ci900397topenalex-snapshot
Protein Pockets: Inventory, Shape, and Comparison
inferredcites →https://doi.org/10.1021/ja026166copenalex-snapshot
Spatial Localization of Ligand Binding Sites from Electron Current Density Surfaces Calculated from NMR Chemical Shift Perturbations
inferredcites →https://doi.org/10.1021/ja039480vopenalex-snapshot
SOS-NMR: A Saturation Transfer NMR-Based Method for Determining the Structures of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm049575nopenalex-snapshot
Identification of Novel p38α MAP Kinase Inhibitors Using Fragment-Based Lead Generation
inferredcites →https://doi.org/10.1021/jm0495778openalex-snapshot
Fragment-Based Lead Discovery Using X-ray Crystallography
inferredcites →https://doi.org/10.1021/jm070095gopenalex-snapshot
Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction
inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1038/nbt1273openalex-snapshot
Structure-based maximal affinity model predicts small-molecule druggability
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
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Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy
inferredcites →https://doi.org/10.1074/jbc.m111305200openalex-snapshot
The Oxidized Lipid and Lipoxygenase Product 12(S)-Hydroxyeicosatetraenoic Acid Induces Hypertrophy and Fibronectin Transcription in Vascular Smooth Muscle Cells via p38 MAPK and cAMP Response Element-binding Protein Activation
inferredcites →https://doi.org/10.1074/jbc.m500418200openalex-snapshot
15(S)-Lipoxygenase-2 Mediates Arachidonic Acid-stimulated Adhesion of Human Breast Carcinoma Cells through the Activation of TAK1, MKK6, and p38 MAPK
inferredcites →https://doi.org/10.1074/jbc.m602177200openalex-snapshot
p38 Mitogen-activated Protein Kinase Mediates Free Fatty Acid-induced Gluconeogenesis in Hepatocytes
inferredcites →https://doi.org/10.1074/jbc.m701108200openalex-snapshot
Phosphatidylinositol Ether Lipid Analogues That Inhibit AKT Also Independently Activate the Stress Kinase, p38α, through MKK3/6-independent and -dependent Mechanisms
inferredcites →https://doi.org/10.1089/omi.2009.0045openalex-snapshot
MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btp562openalex-snapshot
E asy MIF s and S ite H ound : a toolkit for the identification of ligand-binding sites in protein structures
inferredcites →https://doi.org/10.1093/nar/gkp281openalex-snapshot
SITEHOUND-web: a server for ligand binding site identification in protein structures
inferredcites →https://doi.org/10.1110/ps.04964705openalex-snapshot
A computational method for the analysis and prediction of protein:phosphopeptide‐binding sites
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CAVITY SCALING: AUTOMATED REFINEMENT OF CAVITY-AWARE MOTIFS IN PROTEIN FUNCTION PREDICTION
inferredcites →https://doi.org/10.1186/1471-2105-8-s4-s9openalex-snapshot
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.
inferredcites →https://doi.org/10.1186/1472-6807-8-5openalex-snapshot
Fast dynamics perturbation analysis for prediction of protein functional sites
inferredcites →https://doi.org/10.1186/1752-153x-1-7openalex-snapshot
PocketPicker: analysis of ligand binding-sites with shape descriptors
inferredcites →https://doi.org/10.1371/journal.pcbi.1000585openalex-snapshot
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
inferredcites →https://doi.org/10.1371/journal.pcbi.1000634openalex-snapshot
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
inferredcites →https://doi.org/10.2174/138620709789824682openalex-snapshot
Structure-Based Virtual Ligand Screening: Recent Success Stories

What points at this work

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

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Overview of Probing Protein‐Ligand Interactions Using NMR
inferred← citeshttps://doi.org/10.1007/7355_2021_133openalex-snapshot
Protein Labeling and Structure Determination by NMR Spectroscopy
inferred← citeshttps://doi.org/10.1007/s10858-019-00295-9openalex-snapshot
Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra
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Determining binding sites of polycyclic aromatic small molecule-based amyloid-beta peptide aggregation modulators using sequence-specific antibodies
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Exploring the Frontiers of Computational NMR: Methods, Applications, and Challenges
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Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA–Ligand Poses?
inferred← citeshttps://doi.org/10.1021/acschembio.6c00587openalex-snapshot
Chemoenzymatic Proline Isotope Labeling for Solution and Magic-Angle Spinning Protein Nuclear Magnetic Resonance
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The Hitchhiker’s Guide to Deep Learning Driven Generative Chemistry
inferred← citeshttps://doi.org/10.1021/jacs.3c03325openalex-snapshot
μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping
inferred← citeshttps://doi.org/10.1021/jacs.5c06493openalex-snapshot
Assignment-Free Determination of Ligand Binding Sites in Proteins by Solid-State NMR
inferred← citeshttps://doi.org/10.3390/molecules23010148openalex-snapshot
Current NMR Techniques for Structure-Based Drug Discovery
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