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Fragment-Based Lead Discovery Using X-ray Crystallography

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What this work says

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

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Kinase inhibitors and the case for CH…O hydrogen bonds in protein–ligand binding
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Automatic generation of 3D-atomic coordinates for organic molecules
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High-throughput X-ray crystallography for drug discovery
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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
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Cyclin-Dependent KinasesInitial Approaches to Exploit a Novel Therapeutic Target
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Pharmacological inhibitors of cyclin-dependent kinases
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Small, low nanomolar, noncovalent thrombin inhibitors lacking a group to fill the ‘Distal binding pocket’
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The SHAPES strategy: an NMR-based approach for lead generation in drug discovery
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A web-based platform for virtual screening
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Structure-based screening and design in drug discovery
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Structure-based screening of low-affinity compounds
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A ‘Rule of Three’ for fragment-based lead discovery?
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Ligand efficiency: a useful metric for lead selection
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Promiscuity: what protects us, perplexes us
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Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa ,
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Crystal Structures of Ribonuclease A Complexes with 5‘-Diphosphoadenosine 3‘-Phosphate and 5‘-Diphosphoadenosine 2‘-Phosphate at 1.7 Å Resolution,
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Structural Basis for Inhibition of the Protein Tyrosine Phosphatase 1B by Phosphotyrosine Peptide Mimetics,
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Crystal Structures of Thrombin Complexed to a Novel Series of Synthetic Inhibitors Containing a 5,5-trans-Lactone Template
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Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery
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Is There a Difference between Leads and Drugs? A Historical Perspective
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Structure-Based Screening As Applied to Human FABP4: A Highly Efficient Alternative to HTS for Hit Generation
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Discovery of Potent Nonpeptide Inhibitors of Stromelysin Using SAR by NMR
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Novel Inhibitors of DNA Gyrase: 3D Structure Based Biased Needle Screening, Hit Validation by Biophysical Methods, and 3D Guided Optimization. A Promising Alternative to Random Screening
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Crystal Structure of Human Cyclin-Dependent Kinase 2 in Complex with the Adenine-Derived Inhibitor H717
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Structure of Protein Tyrosine Phosphatase 1B in Complex with Inhibitors Bearing Two Phosphotyrosine Mimetics
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SAR and X-ray. A New Approach Combining Fragment-Based Screening and Rational Drug Design: Application to the Discovery of Nanomolar Inhibitors of Src SH2
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Requirements for Specific Binding of Low Affinity Inhibitor Fragments to the SH2 Domain ofpp60Src Are Identical to Those for High Affinity Binding of Full Length Inhibitors
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Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization
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Identification of Novel p38α MAP Kinase Inhibitors Using Fragment-Based Lead Generation
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The Properties of Known Drugs. 1. Molecular Frameworks
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High-Resolution Crystal Structures of Human Cyclin-Dependent Kinase 2 with and without ATP: Bound Waters and Natural Ligand as Guides for Inhibitor Design
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Design and Synthesis of a Series of Potent and Orally Bioavailable Noncovalent Thrombin Inhibitors That Utilize Nonbasic Groups in the P1 Position
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Properties of Known Drugs. 2. Side Chains
inferredcites →https://doi.org/10.1023/a:1022446720849openalex-snapshot
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
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AstexViewerTM †: a visualisation aid for structure-based drug design
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Discovering novel ligands for macromolecules using X-ray crystallographic screening
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Ligation-mediated PCR for quantitative in vivo footprinting
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Structural basis for p38α MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity
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Science, art and drug discovery: a personal perspective
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The structure of mitogen-activated protein kinase p38 at 2.1-Å resolution
inferredcites →https://doi.org/10.1073/pnas.97.17.9367openalex-snapshot
Site-directed ligand discovery
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Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src inhibitors
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Acquisition of Sensitivity of Stress-activated Protein Kinases to the p38 Inhibitor, SB 203580, by Alteration of One or More Amino Acids within the ATP Binding Pocket
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2-(Oxalylamino)-Benzoic Acid Is a General, Competitive Inhibitor of Protein-tyrosine Phosphatases
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/protein/3.1.1openalex-snapshot
The price of lost freedom: entropy of bimolecular complex formation
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Thrombin structure and function
inferredcites →https://doi.org/10.1107/s0108767393007597openalex-snapshot
AMoRe: an automated package for molecular replacement
inferredcites →https://doi.org/10.1107/s0907444996012255openalex-snapshot
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
inferredcites →https://doi.org/10.1107/s0907444998003254openalex-snapshot
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
inferredcites →https://doi.org/10.1107/s090744499900935xopenalex-snapshot
The finer things in X-ray diffraction data collection
inferredcites →https://doi.org/10.1110/ps.9.6.1217openalex-snapshot
Productive and nonproductive binding to ribonuclease A: X‐ray structure of two complexes with uridylyl(2′,5′)guanosine
inferredcites →https://doi.org/10.1126/science.1650499openalex-snapshot
Protein Tyrosine Phosphatases: A Diverse Family of Intracellular and Transmembrane Enzymes
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Inhibitors of Cyclin-Dependent Kinases as Anti-Cancer Therapeutics
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Inhibitors of p38 MAP Kinase: Therapeutic Intervention in Cytokine-Mediated Diseases

What points at this work

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

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Cell wall target fragment discovery using a low‐cost, minimal fragment library
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Fragment‐based drug discovery—the importance of high‐quality molecule libraries
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Combinatorial Libraries: Applications in Chemical Biology
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Strategies for Discovering Kinase Drugs
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Preclinical Drug Development Planning
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Fragment‐Based Lead Discovery
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Fragment‐Based Drug Design: Considerations for Good ADME Properties
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SPR‐Based Direct Binding Assays in Drug Discovery
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A Structural View on Druggability
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Combinatorial Chemistry Library Design
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Advances in X‐Ray Diffraction
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The Target Family Approach
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Fragment‐Based Approaches in Virtual Screening
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PlasmodiumHsp90 as an Antimalarial Target
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Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein–Ligand Binding Affinity
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Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein–Ligand Binding Affinity
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Fragment Deconstruction of Small, Potent Factor Xa Inhibitors: Exploring the Superadditivity Energetics of Fragment Linking in Protein–Ligand Complexes
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Repositioning the Substrate Activity Screening (SAS) Approach as a Fragment‐Based Method for Identification of Weak Binders
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Automated Protein–Ligand Crystallography for Structure‐Based Drug Design
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Fragment‐Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition
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A Comprehensive Structural Overview of p38α MAPK in Complex with Type I Inhibitors
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Fragment‐based quantitative structure–activity relationship (FB‐QSAR) for fragment‐based drug design
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Accurate prediction of dynamic protein–ligand binding using P‐score ranking
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Protocol for Fragment Hopping
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Fragment-Based Ligand Designing
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Organizing Bioactive Compound Discovery in Target Families
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Design of Screening Collections for Successful Fragment-Based Lead Discovery
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Design of compound libraries for fragment screening
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Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
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The multiple roles of computational chemistry in fragment-based drug design
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Challenges of fragment screening
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Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics
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Determination of ligand binding modes in weak protein–ligand complexes using sparse NMR data
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Structural genomics of protein phosphatases
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Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei
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Multitargeting Heterocycles
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Fragment-Based Drug Discovery
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Protein Crystallography and Drug Discovery
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Key Factors for Successful Generation of Protein–Fragment Structures
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Predicting the Success of Fragment Screening by X-Ray Crystallography
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Using Computational Techniques in Fragment-Based Drug Discovery
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Practical Aspects of NMR-Based Fragment Screening
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Fragment Screening Purely with Protein Crystallography
inferred← citeshttps://doi.org/10.1016/b978-0-12-381274-2.00016-9openalex-snapshot
Medicinal Chemistry Inspired Fragment-Based Drug Discovery
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Fragment Screening of Infectious Disease Targets in a Structural Genomics Environment
inferred← citeshttps://doi.org/10.1016/b978-0-12-382030-3.00002-7openalex-snapshot
Lead Discovery and Lead Modification
inferred← citeshttps://doi.org/10.1016/b978-0-12-396521-9.00004-8openalex-snapshot
Structural Biology and Anticancer Drug Design
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.02568-3openalex-snapshot
Library Design: Reactant and Product-Based Approaches
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12317-0openalex-snapshot
High-Throughput Crystallography and Its Applications in Drug Discovery
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12319-4openalex-snapshot
Fragment-Based Drug Design: Strategic Advances and Lessons Learned
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12392-3openalex-snapshot
Protein–Protein Interaction Inhibitors in Cancer
inferred← citeshttps://doi.org/10.1016/b978-0-12-411508-8.00005-0openalex-snapshot
Medicinal Chemistry
inferred← citeshttps://doi.org/10.1016/b978-0-12-417205-0.00007-9openalex-snapshot
Fragment-Based Drug Discovery
inferred← citeshttps://doi.org/10.1016/b978-0-12-803959-5.50004-0openalex-snapshot
Towards Small Molecules as Therapies for Alzheimer’s Disease and Other Neurodegenerative Disorders
inferred← citeshttps://doi.org/10.1016/b978-0-12-817214-8.00005-1openalex-snapshot
Medicinal chemistry
inferred← citeshttps://doi.org/10.1016/b978-0-12-819132-3.00013-0openalex-snapshot
Structure-guided discovery of pharmacological chaperones targeting protein conformational and misfolding diseases
inferred← citeshttps://doi.org/10.1016/b978-0-443-15862-9.00002-3openalex-snapshot
Lead Discovery
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00067-4openalex-snapshot
Protein-protein interaction inhibitors in cancer
inferred← citeshttps://doi.org/10.1016/b978-0-7020-4299-7.00008-1openalex-snapshot
High-throughput screening
inferred← citeshttps://doi.org/10.1016/b978-012369448-5.50007-0openalex-snapshot
Structural biology and anticancer drug design
inferred← citeshttps://doi.org/10.1016/b978-012369448-5.50014-8openalex-snapshot
Cell cycle inhibitors in cancer: current status and future directions
inferred← citeshttps://doi.org/10.1016/bs.mie.2018.08.016openalex-snapshot
Applications of Dissolution-DNP for NMR Screening
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Achieving a Good Crystal System for Crystallographic X-Ray Fragment Screening
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Biophysical screening and characterisation in medicinal chemistry
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Capillary electrophoretic mobility shift displacement assay for the assessment of weak drug-protein interactions
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Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor
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Structure-guided expansion of kinase fragment libraries driven by support vector machine models
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Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review
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Recent updates on development of protein-tyrosine phosphatase 1B inhibitors for treatment of diabetes, obesity and related disorders
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.09.055openalex-snapshot
Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.11.025openalex-snapshot
Identification of a novel ligand binding motif in the transthyretin channel
inferred← citeshttps://doi.org/10.1016/j.bmc.2010.01.055openalex-snapshot
Novel thiophene derivatives as PTP1B inhibitors with selectivity and cellular activity
inferred← citeshttps://doi.org/10.1016/j.bmc.2015.01.013openalex-snapshot
Cell-based and virtual fragment screening for adrenergic α2C receptor agonists
inferred← citeshttps://doi.org/10.1016/j.bmc.2022.116879openalex-snapshot
Fragment hopping protocol for the design of small-molecule protein–protein interaction inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2008.03.056openalex-snapshot
Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2011.04.027openalex-snapshot
The identification of new metallo-β-lactamase inhibitor leads from fragment-based screening
inferred← citeshttps://doi.org/10.1016/j.bmcl.2016.03.003openalex-snapshot
Novel Imbricatolic acid derivatives as protein tyrosine phosphatase-1B inhibitors: Design, synthesis, biological evaluation and molecular docking
inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.10.054openalex-snapshot
The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design
inferred← citeshttps://doi.org/10.1016/j.bpj.2025.03.016openalex-snapshot
Mapping the distribution and affinities of ligand interaction sites on human serum albumin
inferred← citeshttps://doi.org/10.1016/j.cbpa.2005.05.002openalex-snapshot
Fragonomics: fragment-based drug discovery
inferred← citeshttps://doi.org/10.1016/j.cbpa.2005.06.007openalex-snapshot
Recent applications of protein crystallography and structure-guided drug design
inferred← citeshttps://doi.org/10.1016/j.cbpa.2006.06.003openalex-snapshot
How good is your screening library?
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The interdependence between screening methods and screening libraries
inferred← citeshttps://doi.org/10.1016/j.cbpa.2007.07.010openalex-snapshot
Fragment-based screening using X-ray crystallography and NMR spectroscopy
inferred← citeshttps://doi.org/10.1016/j.chembiol.2005.08.013openalex-snapshot
Solution Nuclear Magnetic Resonance Spectroscopy Techniques for Probing Intermolecular Interactions
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Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures
inferred← citeshttps://doi.org/10.1016/j.copbio.2005.10.007openalex-snapshot
Improving success rates for lead generation using affinity binding technologies
inferred← citeshttps://doi.org/10.1016/j.copbio.2006.10.007openalex-snapshot
Fragment-based lead discovery: a chemical update
inferred← citeshttps://doi.org/10.1016/j.copbio.2007.09.003openalex-snapshot
Fragment-based approaches to enzyme inhibition
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.12.017openalex-snapshot
Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.ddtec.2006.11.001openalex-snapshot
High throughput protein crystallography: Developments in crystallisation, data collection and data processing
inferred← citeshttps://doi.org/10.1016/j.ddtec.2006.12.001openalex-snapshot
The fragment-approach: An update
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Fragments: past, present and future
inferred← citeshttps://doi.org/10.1016/j.ddtec.2010.11.010openalex-snapshot
Fragment library design: efficiently hunting drugs in chemical space
inferred← citeshttps://doi.org/10.1016/j.drudis.2006.02.008openalex-snapshot
Integrating molecular design resources within modern drug discovery research: the Roche experience
inferred← citeshttps://doi.org/10.1016/j.drudis.2006.06.016openalex-snapshot
Hit discovery and hit-to-lead approaches
inferred← citeshttps://doi.org/10.1016/j.drudis.2007.03.011openalex-snapshot
PTP1B as a drug target: recent developments in PTP1B inhibitor discovery
inferred← citeshttps://doi.org/10.1016/j.drudis.2007.07.006openalex-snapshot
The role of quantum mechanics in structure-based drug design
inferred← citeshttps://doi.org/10.1016/j.drudis.2007.08.005openalex-snapshot
Integration of fragment screening and library design
inferred← citeshttps://doi.org/10.1016/j.drudis.2008.02.004openalex-snapshot
Application of technologies and parallel chemistry for the generation of actives against biological targets
inferred← citeshttps://doi.org/10.1016/j.drudis.2009.03.009openalex-snapshot
Transforming fragments into candidates: small becomes big in medicinal chemistry
inferred← citeshttps://doi.org/10.1016/j.drudis.2009.04.007openalex-snapshot
From fragment to clinical candidate—a historical perspective
inferred← citeshttps://doi.org/10.1016/j.drudis.2011.08.002openalex-snapshot
The role of fragment-based and computational methods in polypharmacology
inferred← citeshttps://doi.org/10.1016/j.drudis.2014.09.015openalex-snapshot
Evolutions in fragment-based drug design: the deconstruction–reconstruction approach
inferred← citeshttps://doi.org/10.1016/j.drudis.2018.05.004openalex-snapshot
When fragments link: a bibliometric perspective on the development of fragment-based drug discovery
inferred← citeshttps://doi.org/10.1016/j.drudis.2019.03.009openalex-snapshot
Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design
inferred← citeshttps://doi.org/10.1016/j.drudis.2019.12.006openalex-snapshot
Fragment-based drug discovery using cryo-EM
inferred← citeshttps://doi.org/10.1016/j.ejmech.2008.08.012openalex-snapshot
Fragment and knowledge-based design of selective GSK-3β inhibitors using virtual screening models
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.05.027openalex-snapshot
Synthesis and biological evaluation of (±)-3-(2-(2-fluorobenzyloxy) naphthalen-6-yl)-2-aminopropanoic acid derivatives as novel PTP1B inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.06.025openalex-snapshot
Click to a focused library of benzyl 6-triazolo(hydroxy)benzoic glucosides: Novel construction of PTP1B inhibitors on a sugar scaffold
inferred← citeshttps://doi.org/10.1016/j.ejmech.2019.02.011openalex-snapshot
Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114105openalex-snapshot
A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen)
inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.116960openalex-snapshot
Rational fragment-based design of compounds targeting the PWWP domain of the HRP family
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.119251openalex-snapshot
Critical structural insights into selective small-molecule and peptide inhibitors of human urokinase-type plasminogen activator
inferred← citeshttps://doi.org/10.1016/j.ejps.2015.05.001openalex-snapshot
Establish an automated flow injection ESI-MS method for the screening of fragment based libraries: Application to Hsp90
inferred← citeshttps://doi.org/10.1016/j.febslet.2007.09.051openalex-snapshot
Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue
inferred← citeshttps://doi.org/10.1016/j.gde.2009.10.010openalex-snapshot
Scaffold-based design of kinase inhibitors for cancer therapy
inferred← citeshttps://doi.org/10.1016/j.jmb.2012.03.012openalex-snapshot
Fragmentation-Tree Density Representation for Crystallographic Modelling of Bound Ligands
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Proposing novel TNFα direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline
inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.136475openalex-snapshot
Synthesis, crystal structure characterization and computational investigation of new thieno[2,3-b]pyridine derivatives as potent against molecule p38 alpha MAP kinase
inferred← citeshttps://doi.org/10.1016/j.mrl.2021.100025openalex-snapshot
Recent progress in fragment-based drug discovery facilitated by NMR spectroscopy
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Advantages of crystallographic fragment screening: Functional and mechanistic insights from a powerful platform for efficient drug discovery
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Can we rationally design promiscuous drugs?
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Different applications and differentiated libraries for crystallographic fragment screening
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New Dimensions of Structural Proteomics: Exploring Chemical and Biological Space
inferred← citeshttps://doi.org/10.1016/j.str.2024.05.011openalex-snapshot
Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design
inferred← citeshttps://doi.org/10.1016/j.tet.2012.08.062openalex-snapshot
Synthesis of a biphenyl library for studies of hydrogen bonding in the solid state
inferred← citeshttps://doi.org/10.1016/j.tetlet.2011.07.147openalex-snapshot
Synthesis and solid state study of pyridine- and pyrimidine-based fragment libraries
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Diversity-oriented synthesis of N,N -dimethylamino-substituted azoles employing TBTU
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Structure-based design of molecular cancer therapeutics
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Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery
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Review of the impact of fragment-based drug design on PROTAC degrader discovery
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Crystallization of MAP kinases
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery
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Structural Genomics and Drug Discovery
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Chapter 28 Fragment-Based Lead Discovery
inferred← citeshttps://doi.org/10.1016/s0079-6468(05)44401-xopenalex-snapshot
1 Finding Protein Kinase Hits using Structural Information
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1Hit and Lead Identification: Efficient Practices for Drug Discovery
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287 POSTER Fragment-based discovery of AT9283; a multi-targeted kinase inhibitor with potent Aurora kinase activity
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Keynote review: Structural biology and drug discovery
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Widening bottlenecks in drug discovery Glimpses from Drug Discovery Technology Europe 2005
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Fragment-based lead discovery: leads by design
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Microarrays, databases and hard, hard sums
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