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Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method

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What this work says

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

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A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

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Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

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Maximum common subgraph isomorphism algorithms and their applications in molecular science: a review

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Predicting the Performance of Fingerprint Similarity Searching

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BACE-1 inhibitors part 3: Identification of hydroxy ethylamines (HEAs) with nanomolar potency in cells

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Design and synthesis of cell potent BACE-1 inhibitors: Structure–activity relationship of P1′ substituents

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Structure-based design and synthesis of novel P2/P3 modified, non-peptidic β-secretase (BACE-1) inhibitors

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Novel pyrrolyl 2-aminopyridines as potent and selective human β-secretase (BACE1) inhibitors

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Piperazine sulfonamide BACE1 inhibitors: Design, synthesis, and in vivo characterization

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Fragment-based discovery and optimization of BACE1 inhibitors

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Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors

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Aminoimidazoles as BACE-1 inhibitors: The challenge to achieve in vivo brain efficacy

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Structure-based design of novel dihydroisoquinoline BACE-1 inhibitors that do not engage the catalytic aspartates

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Virtual ligand screening: strategies, perspectives and limitations

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Quaternions in molecular modeling

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Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

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Geometry optimization methods for modeling large molecules

inferredcites →https://doi.org/10.1021/ci00011a016openalex-snapshot

Rapid evaluation of shape similarity using Gaussian functions

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Flexible 3D searching: The directed tweak technique

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Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and β-Secretase

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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers

inferredcites →https://doi.org/10.1021/ci100062nopenalex-snapshot

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

inferredcites →https://doi.org/10.1021/ci100136bopenalex-snapshot

One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space

inferredcites →https://doi.org/10.1021/ci100263popenalex-snapshot

Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods

inferredcites →https://doi.org/10.1021/ci2002704openalex-snapshot

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring

inferredcites →https://doi.org/10.1021/ci2003544openalex-snapshot

Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

inferredcites →https://doi.org/10.1021/ci200528dopenalex-snapshot

Recognizing Pitfalls in Virtual Screening: A Critical Review

inferredcites →https://doi.org/10.1021/ci200617dopenalex-snapshot

Ligand-Based Virtual Screening Approach Using a New Scoring Function

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Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening

inferredcites →https://doi.org/10.1021/ci300083ropenalex-snapshot

Protein–Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling

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Protein Flexibility in Virtual Screening: The BACE-1 Case Study

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Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking

inferredcites →https://doi.org/10.1021/ci300547gopenalex-snapshot

Combination of Similarity Rankings Using Data Fusion

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Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem

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Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches

inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/ci700130jopenalex-snapshot

A Comparison of Field-Based Similarity Searching Methods: CatShape, FBSS, and ROCS

inferredcites →https://doi.org/10.1021/ci700223popenalex-snapshot

Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1)

inferredcites →https://doi.org/10.1021/ci800249sopenalex-snapshot

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

inferredcites →https://doi.org/10.1021/ci800303kopenalex-snapshot

Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set

inferredcites →https://doi.org/10.1021/ci8004226openalex-snapshot

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information

inferredcites →https://doi.org/10.1021/ci900015bopenalex-snapshot

Unconventional 2D Shape Similarity Method Affords Comparable Enrichment as a 3D Shape Method in Virtual Screening Experiments

inferredcites →https://doi.org/10.1021/ci900419kopenalex-snapshot

Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation

inferredcites →https://doi.org/10.1021/ci900507gopenalex-snapshot

Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment

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DREIDING: a generic force field for molecular simulations

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Virtual Screening for β-Secretase (BACE1) Inhibitors Reveals the Importance of Protonation States at Asp32 and Asp228

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot

Comparison of Shape-Matching and Docking as Virtual Screening Tools

inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot

Benchmarking Sets for Molecular Docking

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From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1)

inferredcites →https://doi.org/10.1021/jm300069yopenalex-snapshot

Discovery of Cyclic Sulfone Hydroxyethylamines as Potent and Selective β-Site APP-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure-Based Design and in Vivo Reduction of Amyloid β-Peptides

inferredcites →https://doi.org/10.1021/jm300687eopenalex-snapshot

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

inferredcites →https://doi.org/10.1021/jm3009025openalex-snapshot

Design and Synthesis of β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors with in Vivo Brain Reduction of β-Amyloid Peptides

inferredcites →https://doi.org/10.1021/jm301039copenalex-snapshot

Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation

inferredcites →https://doi.org/10.1021/jm800914nopenalex-snapshot

Discovery and X-ray Crystallographic Analysis of a Spiropiperidine Iminohydantoin Inhibitor of β-Secretase

inferredcites →https://doi.org/10.1021/jm900818sopenalex-snapshot

Molecular Shape and Medicinal Chemistry: A Perspective

inferredcites →https://doi.org/10.1021/jm901408popenalex-snapshot

Discovery of Cyclic Acylguanidines as Highly Potent and Selective β-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I—Inhibitor Design and Validation

inferredcites →https://doi.org/10.1021/jm901414eopenalex-snapshot

Design and Synthesis of 5,5′-Disubstituted Aminohydantoins as Potent and Selective Human β-Secretase (BACE1) Inhibitors

inferredcites →https://doi.org/10.1021/jm981037lopenalex-snapshot

F lex S: A Method for Fast Flexible Ligand Superposition

inferredcites →https://doi.org/10.1021/ml3000148openalex-snapshot

A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of β-Secretase

inferredcites →https://doi.org/10.1080/00268979100100941openalex-snapshot

Analytical treatment of the volume and surface area of molecules formed by an arbitrary collection of unequal spheres intersected by planes

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The structure of the Bach2 POZ-domain dimer reveals an intersubunit disulfide bond

inferredcites →https://doi.org/10.1107/s0907444913006574openalex-snapshot

Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones

inferredcites →https://doi.org/10.1201/9781420028775openalex-snapshot

Virtual Screening in Drug Discovery

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Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17

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