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Automated Protein–Ligand Crystallography for Structure‐Based Drug Design

https://doi.org/10.1002/cmdc.200600074

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What this work says

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

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Flexible docking using tabu search and an empirical estimate of binding affinity

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Optimization of parameters for semiempirical methods I. Method

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A new test set for validating predictions of protein–ligand interaction

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Improved protein–ligand docking using GOLD

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

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Automatic generation of 3D-atomic coordinates for organic molecules

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Applications for Macromolecular Map Interpretation: X-AUTOFIT, X-POWERFIT, X-BUILD, X-LIGAND, and X-SOLVATE

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[23] Bayesian statistical viewpoint on structure determination: Basic concepts and examples

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Automated Crystal Mounting and Data Collection for Protein Crystallography

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LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

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Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

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Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

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Identification of Novel p38α MAP Kinase Inhibitors Using Fragment-Based Lead Generation

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Fragment-Based Lead Discovery Using X-ray Crystallography

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Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors

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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

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AstexViewerTM †: a visualisation aid for structure-based drug design

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Current state of automated crystallographic data analysis.

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Automated protein model building combined with iterative structure refinement.

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High-throughput protein crystallography and drug discovery

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The Protein Data Bank

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Improved Fourier coefficients for maps using phases from partial structures with errors

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AMoRe: an automated package for molecular replacement

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Pushing the boundaries of molecular replacement with maximum likelihood

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Automated structure solution, density modification and model building

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PHENIX : building new software for automated crystallographic structure determination

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Automated crystallographic system for high-throughput protein structure determination

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PRODRG: a tool for high-throughput crystallography of protein–ligand complexes

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Modelling bound ligands in protein crystal structures

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The Uppsala Electron-Density Server

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Refinement of severely incomplete structures with maximum likelihood inBUSTER–TNT

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Coot : model-building tools for molecular graphics

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Interactive electron-density map interpretation: fromINTERtoO

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The CCP4 suite: programs for protein crystallography

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Databases in Protein Crystallography

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JIT's Impact on a Firm's Financial Statements

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

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The Pyramid™ Approach to Fragment‐Based Biophysical Screening

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High‐Throughput Macromolecular Crystallography in Drug Discovery

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De Novo Design by Fragment Growing and Docking

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QM/MM refinement and analysis of protein bound retinoic acid

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Fragment Screening Using X-Ray Crystallography

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Fragment-Based Drug Discovery Using Rational Design

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The Use of Molecular Graphics in Structure-Based Drug Design

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Crystallographic Fragment Screening

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Methods for Rational Design and Discovery of Multitarget Drugs

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Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors

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Structural genomics of protein phosphatases

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Protein Crystallography and Drug Discovery

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Local heterogeneity analysis of crystallographic and cryo-EM maps using shell-approximation

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High throughput protein crystallography: Developments in crystallisation, data collection and data processing

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The fragment-approach: An update

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Transforming fragments into candidates: small becomes big in medicinal chemistry

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Homology modeling in drug discovery: current trends and applications

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High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits

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Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design

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High throughput cryo-EM provides structural understanding for modulators of the lysosomal ion channel TRPML1

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Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures

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Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein–Protein Interaction

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Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein−Protein Interaction

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Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2)

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Fragment-Based Discovery of a Series of Allosteric-Binding Site Modulators of β-Glucocerebrosidase

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Structure–Activity and Structure–Conformation Relationships of Aryl Propionic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1/Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1/NRF2) Protein–Protein Interaction

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Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study

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PDB Ligand Conformational Energies Calculated Quantum-Mechanically

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Conformational Variability of Benzamidinium-Based Inhibitors

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Automated identification of crystallographic ligands using sparse-density representations

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TheXChemExplorergraphical workflow tool for routine or large-scale protein–ligand structure determination

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Real-space refinement in PHENIX for cryo-EM and crystallography

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Direct calculation of cryo-EM and crystallographic model maps for real-space refinement

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