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Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening

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

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Modeling Promiscuity Based on in vitro Safety Pharmacology Profiling Data
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TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time
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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
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Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
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In silico repositioning of approved drugs for rare and neglected diseases
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The role of fragment-based and computational methods in polypharmacology
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Drug discovery in pharmaceutical industry: productivity challenges and trends
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In silico drug repositioning – what we need to know
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Shifting from the single to the multitarget paradigm in drug discovery
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Novel paradigms for drug discovery: computational multitarget screening
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Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand–protein inverse docking approach
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SMILES. 2. Algorithm for generation of unique SMILES notation
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ReverseScreen3D: A Structure-Based Ligand Matching Method To Identify Protein Targets
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NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats
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Structural Properties of Non-Traditional Drug Targets Present New Challenges for Virtual Screening
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Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional Protein Libraries: Methods and Problems
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Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
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Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds
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Do Structurally Similar Ligands Bind in a Similar Fashion?
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In Silico-Guided Target Identification of a Scaffold-Focused Library: 1,3,5-Triazepan-2,6-diones as Novel Phospholipase A2 Inhibitors
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Benchmarking Sets for Molecular Docking
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Bridging Chemical and Biological Space: “Target Fishing” Using 2D and 3D Molecular Descriptors
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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
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Rational Approaches to Improving Selectivity in Drug Design
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Relating protein pharmacology by ligand chemistry
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Protein promiscuity and its implications for biotechnology
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Network pharmacology: the next paradigm in drug discovery
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Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia
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Drug repositioning: identifying and developing new uses for existing drugs
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In silicopharmacology for drug discovery: applications to targets and beyond
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The topology of drug–target interaction networks: implicit dependence on drug properties and target families
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sc-PDB: a database for identifying variations and multiplicity of ‘druggable’ binding sites in proteins
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The Protein Data Bank
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TTD: Therapeutic Target Database
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DrugBank: a comprehensive resource for in silico drug discovery and exploration
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TarFisDock: a web server for identifying drug targets with docking approach
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Drug Target Identification Using Side-Effect Similarity
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A chemogenomics view on protein-ligand spaces
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PDTD: a web-accessible protein database for drug target identification
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MONA – Interactive manipulation of molecule collections
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Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes
inferredcites →https://doi.org/10.1371/journal.pcbi.1000441openalex-snapshot
Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
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Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study
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A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs

What points at this work

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

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