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Fragment-Based Approaches and Computer-Aided Drug Discovery

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

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The multiple roles of computational chemistry in fragment-based drug design
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The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
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Fragment-based drug discovery
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Fragment screening of inhibitors for MIF tautomerase reveals a cryptic surface binding site
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Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel
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Integration of fragment screening and library design
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Two ‘Golden Ratio’ indices in fragment-based drug discovery
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Managing protein flexibility in docking and its applications
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Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation
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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing
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eHiTS: A new fast, exhaustive flexible ligand docking system
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
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Discovery of novel low molecular weight inhibitors of IMPDH via virtual needle screening
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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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Molecular Complexity and Its Impact on the Probability of Finding Leads for Drug Discovery
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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment
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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
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Design and Characterization of Libraries of Molecular Fragments for Use in NMR Screening against Protein Targets
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Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
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Mining a Chemical Database for Fragment Co-occurrence: Discovery of “Chemical Clichés”
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Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
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Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases
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Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations
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Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes
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Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
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Chemical Fragment Spaces for de novo Design
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Identification and Selection of “Privileged Fragments” Suitable for Primary Screening
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Identifying and Characterizing Binding Sites and Assessing Druggability
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In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design
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QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors
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Fragment-Based Prediction of the Clinical Occurrence of Long QT Syndrome and Torsade de Pointes
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Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
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970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13
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Structure-Based de Novo Design, Synthesis, and Biological Evaluation of Non-Azole Inhibitors Specific for Lanosterol 14α-Demethylase of Fungi
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Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
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Probing Hot Spots at Protein−Ligand Binding Sites: A Fragment-Based Approach Using Biophysical Methods
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“Virtual Fragment Linking”: An Approach To Identify Potent Binders from Low Affinity Fragment Hits
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Recent Developments in Fragment-Based Drug Discovery
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Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints
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Kinase Inhibitor Data Modeling and de Novo Inhibitor Design with Fragment Approaches
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Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors
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Entropic Contribution to the Linking Coefficient in Fragment Based Drug Design: A Case Study
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A Study of the Active Site of Influenza Virus Sialidase: An Approach to the Rational Design of Novel Anti-influenza Drugs
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Design of a High Fragment Efficiency Library by Molecular Graph Theory
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Molecular docking and ligand specificity in fragment-based inhibitor discovery
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Docking for fragment inhibitors of AmpC β-lactamase
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Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques
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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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