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Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Derivation of Dihedral Angles from CH–CH Dipolar–Dipolar Cross‐Correlated Relaxation Rates: A C–C Torsion Involving a Quaternary Carbon Atom in Epothilone A Bound to Tubulin

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NMR Spectroscopy Techniques for Screening and Identifying Ligand Binding to Protein Receptors

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The INPHARMA Method: Protein‐Mediated Interligand NOEs for Pharmacophore Mapping

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Structural Basis of the Activity of the Microtubule‐Stabilizing Agent Epothilone A Studied by NMR Spectroscopy in Solution

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Crystallography‐Independent Determination of Ligand Binding Modes

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Development and testing of a general amber force field

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Competition STD NMR for the detection of high‐affinity ligands and NMR‐based screening

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Blind docking of pharmaceutically relevant compounds using RosettaLigand

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NMR View: A computer program for the visualization and analysis of NMR data

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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

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An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

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A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

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An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude

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Theory and applications of the transferred nuclear overhauser effect to the study of the conformations of small ligands bound to proteins

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Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

inferredcites →https://doi.org/10.1016/j.jmb.2008.11.010openalex-snapshot

RosettaLigand Docking with Full Ligand and Receptor Flexibility

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The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method

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Flexible ligand docking to multiple receptor conformations: a practical alternative

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Accommodating Protein Flexibility in Computational Drug Design,

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Intrinsically unstructured proteins

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Use of the Transferred Nuclear Overhauser Effect To Determine the Conformations of Ligands Bound to Proteins

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Efficient Drug Lead Discovery and Optimization

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Protein−Ligand Docking against Non-Native Protein Conformers

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Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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Determination of Aliphatic Side-Chain Conformation Using Cross-Correlated Relaxation: Application to an Extraordinarily Stable 2‘-aminoethoxy-Modified Oligonucleotide Triplex

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Group Epitope Mapping by Saturation Transfer Difference NMR To Identify Segments of a Ligand in Direct Contact with a Protein Receptor

inferredcites →https://doi.org/10.1021/ja047695eopenalex-snapshot

Pose Scoring by NMR

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Protein−Ligand NOE Matching: A High-Throughput Method for Binding Pose Evaluation That Does Not Require Protein NMR Resonance Assignments

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Rapid Protein−Ligand Costructures Using Chemical Shift Perturbations

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Efficient Discovery of Potent Anti-HIV Agents Targeting the Tyr181Cys Variant of HIV Reverse Transcriptase

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Analysis of Chemical Shift Changes Reveals the Binding Modes of Isoindolinone Inhibitors of the MDM2-p53 Interaction

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Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy

inferredcites →https://doi.org/10.1021/jm048972vopenalex-snapshot

Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

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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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Do Structurally Similar Ligands Bind in a Similar Fashion?

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Target Flexibility: An Emerging Consideration in Drug Discovery and Design

inferredcites →https://doi.org/10.1023/a:1008360208627openalex-snapshot

The inter-ligand Overhauser effect: A powerful new NMR approach for mapping structural relationships of macromolecular ligands

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Dynamic personalities of proteins

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A decade of fragment-based drug design: strategic advances and lessons learned

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Perspectives on NMR in drug discovery: a technique comes of age

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Is one solution good enough?

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Spin echo NMR spectra without J modulation

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NMR in natural products: understanding conformation, configuration and receptor interactions

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Dynamics and function of proteins: The search for general concepts

inferredcites →https://doi.org/10.1074/jbc.271.42.26157openalex-snapshot

Crystal Structures of Catalytic Subunit of cAMP-dependent Protein Kinase in Complex with Isoquinolinesulfonyl Protein Kinase Inhibitors H7, H8, and H89

inferredcites →https://doi.org/10.1089/10665270360688228openalex-snapshot

Understanding Protein Flexibility through Dimensionality Reduction

inferredcites →https://doi.org/10.1093/bioinformatics/btl461openalex-snapshot

Bio3d: an R package for the comparative analysis of protein structures

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The Protein Data Bank

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A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics

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The Many Roles of Computation in Drug Discovery

inferredcites →https://doi.org/10.1146/annurev.biophys.34.040204.144419openalex-snapshot

Ligand-Target Interactions: What Can We Learn from NMR?

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/10.2174/138161211796355056openalex-snapshot

Molecular Recognition in the Case of Flexible Targets

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Dynamics, Flexibility and Ligand-Induced Conformational Changes in Biological Macromolecules: A Computational Approach

What points at this work

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

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NMR Studies of Protein–Small Molecule Interactions for Drug Discovery

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The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X‐ray Crystallography

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INPHARMA‐Based Determination of Ligand Binding Modes at α1‐Adrenergic Receptors Explains the Molecular Basis of Subtype Selectivity

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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

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NMR‐Assisted Molecular Docking Methodologies

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Protein–Ligand Interactions Studied by NMR

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Protein–Ligand Interactions Studied by NMR

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The role of small-angle scattering in structure-based screening applications

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On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein–Ligand Docking

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Structure-Based Design of Scaffolds Targeting PDE10A by INPHARMA-NMR

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Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review

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Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA

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Performance of Protein–Ligand Docking with Simulated Chemical Shift Perturbations

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Structure-based design of human pancreatic amylase inhibitors from the natural anthocyanin database for type 2 diabetes

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Estudos estruturais e de interação de novos inibidores e ativadores da tirosinase

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