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Considerations in Compound Database Preparation“Hidden” Impact on Virtual Screening Results

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What this work says

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

inferredcites →https://doi.org/10.1002/prot.20149openalex-snapshot

Comparative evaluation of eight docking tools for docking and virtual screening accuracy

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools

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Basic Guide to the Mechanisms of Antiestrogen Action

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The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of This Interaction by Tamoxifen

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The price of innovation: new estimates of drug development costs

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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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Molecular similarity-based estimation of properties: a comparison of three structure spaces

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Consensus scoring for ligand/protein interactions

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Assessing the performance of OMEGA with respect to retrieving bioactive conformations

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Statistical intelligence: effective analysis of high-density microarray data

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How many leads from HTS?

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

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Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment

inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot

Detailed Analysis of Scoring Functions for Virtual Screening

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

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Flexible Estrogen Receptor Modulators: Design, Synthesis, and Antagonistic Effects in Human MCF-7 Breast Cancer Cells

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Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B

inferredcites →https://doi.org/10.1021/jm0300173openalex-snapshot

Nuclear Hormone Receptor Targeted Virtual Screening

inferredcites →https://doi.org/10.1021/jm030563wopenalex-snapshot

Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding

inferredcites →https://doi.org/10.1021/jm034222uopenalex-snapshot

Scaffold Hopping in De Novo Design. Ligand Generation in the Absence of Receptor Information

inferredcites →https://doi.org/10.1021/jm0495834openalex-snapshot

Benzoxepin-Derived Estrogen Receptor Modulators: A Novel Molecular Scaffold for the Estrogen Receptor

inferredcites →https://doi.org/10.1021/jm990408aopenalex-snapshot

Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads

inferredcites →https://doi.org/10.1023/a:1008158231558openalex-snapshot

Deciphering common failures in molecular docking of ligand-protein complexes

inferredcites →https://doi.org/10.1023/a:1015930826903openalex-snapshot

Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools

inferredcites →https://doi.org/10.1038/37845openalex-snapshot

Library tries to rebuild flooded collection

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Molecular basis of agonism and antagonism in the oestrogen receptor

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The Protein Data Bank and the challenge of structural genomics.

inferredcites →https://doi.org/10.1038/nature03197openalex-snapshot

Virtual screening of chemical libraries

inferredcites →https://doi.org/10.1038/nrd745openalex-snapshot

Chemical database techniques in drug discovery

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Endocrine-dependent Tumors

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From Knowing to Controlling: A Path from Genomics to Drugs Using Small Molecule Probes

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The Many Roles of Computation in Drug Discovery

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Advances in the Science of Estrogen Receptor Modulation

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781118771723.ch9openalex-snapshot

Virtual Screening

inferred← citeshttps://doi.org/10.1002/9783527633326.ch2openalex-snapshot

Preparing and Filtering Compound Databases for Virtual and Experimental Screening

inferred← citeshttps://doi.org/10.1002/9783527633326.ch6openalex-snapshot

Docking Methods for Virtual Screening: Principles and Recent Advances

inferred← citeshttps://doi.org/10.1002/minf.201000034openalex-snapshot

‘tieredScreen’ – Layered Virtual Screening Tool for the Identification of Novel Estrogen Receptor Alpha Modulators

inferred← citeshttps://doi.org/10.1002/minf.201100127openalex-snapshot

Consensus Computational Ligand‐Based Design for the Identification of Novel Modulators of Human Estrogen Receptor Alpha

inferred← citeshttps://doi.org/10.1002/prot.21405openalex-snapshot

Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections

inferred← citeshttps://doi.org/10.1002/qsar.200610089openalex-snapshot

Data Pipelines and Virtual Screening: Automating the Process

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Computational methods for scaffold hopping

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Outstanding challenges in protein–ligand docking and structure‐based virtual screening

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Artificial Intelligence in Compound Design

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Classifying Calpain Inhibitors for the Treatment of Cataracts: A Self Organising Map (SOM) ANN/KM Approach in Drug Discovery

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Permuting input for more effective sampling of 3D conformer space

inferred← citeshttps://doi.org/10.1007/s10822-007-9163-6openalex-snapshot

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

inferred← citeshttps://doi.org/10.1007/s10822-008-9249-9openalex-snapshot

VSDMIP: virtual screening data management on an integrated platform

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Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC

inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00017-5openalex-snapshot

Virtual Libraries for Docking Methods: Guidelines for the Selection and the Preparation

inferred← citeshttps://doi.org/10.1016/j.bmc.2008.09.035openalex-snapshot

Synthesis, biological evaluation, structural–activity relationship, and docking study for a series of benzoxepin-derived estrogen receptor modulators

inferred← citeshttps://doi.org/10.1016/j.bmc.2012.04.062openalex-snapshot

Early phase drug discovery: Cheminformatics and computational techniques in identifying lead series

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Virtual screening strategies in drug discovery

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Understanding nuclear receptors using computational methods

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Molecular docking study of macrocycles as Fk506-binding protein inhibitors

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Purposely engineered drug–target mismatches for entropy-based drug optimization

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Identification of small molecules acting against H1N1 influenza A virus

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Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry

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Novel β-keto–enol Pyrazolic Compounds as Potent Antifungal Agents. Design, Synthesis, Crystal Structure, DFT, Homology Modeling, and Docking Studies

inferred← citeshttps://doi.org/10.1021/ci200528dopenalex-snapshot

Recognizing Pitfalls in Virtual Screening: A Critical Review

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Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations

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Comparison of Topological, Shape, and Docking Methods in Virtual Screening

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The Effect of Ligand-Based Tautomer and Protomer Prediction on Structure-Based Virtual Screening

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Target Specific Virtual Screening: Optimization of an Estrogen Receptor Screening Platform

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Integrated Virtual Screening for the Identification of Novel and Selective Peroxisome Proliferator-Activated Receptor (PPAR) Scaffolds

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Integration of Ligand and Structure-Based Virtual Screening for the Identification of the First Dual Targeting Agent for Heat Shock Protein 90 (Hsp90) and Tubulin

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Virtual Screening for the Identification of Novel Nonsteroidal Glucocorticoid Modulators

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Pharmacore maping based on docking, ADME/toxicity, virtual screening on 3,5-dimethyl-1,3,4-hexanetriol and dodecanoic acid derivates for anticancer inhibitors

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Development of the β-lactam type molecular scaffold for selective estrogen receptor α modulator action: synthesis and cytotoxic effects in MCF-7 breast cancer cells

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FADB: a food additive molecular database forin silicoscreening in food toxicology

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Computational multiscale modeling in protein--ligand docking

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Computational methods and software in computer-aided combinatorial library design

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Calculation of Protein-Ligand Binding Affinities

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Peptides Trapping Dioxins: A Docking‐Based Inverse Screening Approach

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DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

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Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

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Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules

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Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

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Virtual screening of the estrogen receptor

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Virtual screening of chemical libraries for drug discovery

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Harnessing Computational Modeling for Efficient Drug Design Strategies

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The Role of Protonation States in Ligand-Receptor Recognition and Binding

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Development of new virtual screening methods and novel unbiased benchmarking data sets

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Optimisation de méthodes de criblage virtuel et synthèse de molécules à visée thérapeutique pour le traitement des maladies auto-immunes.

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