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

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What this work says

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

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Docking small ligands in flexible binding sites

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Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation

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Ensemble-docking approach on BACE-1: Pharmacophore Perception and Directives for Drug Development

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Integrating Structure‐ and Ligand‐Based Virtual Screening: Comparison of Individual, Parallel, and Fused Molecular Docking and Similarity Search Calculations on Multiple Targets

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Comparison of Structure‐ and Ligand‐Based Virtual Screening Protocols Considering Hit List Complementarity and Enrichment Factors

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A semiempirical free energy force field with charge‐based desolvation

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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

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FlexE: efficient molecular docking considering protein structure variations

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Beta-secretase as a target for Alzheimer’s disease drug discovery: an overview of in vitro methods for characterization of inhibitors

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Protein–ligand docking with multiple flexible side chains

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“Soft docking”: Matching of molecular surface cubes

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Investigation of α-phenylnorstatine and α-benzylnorstatine as transition state isostere motifs in the search for new BACE-1 inhibitors

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Structure-based design of cycloamide–urethane-derived novel inhibitors of human brain memapsin 2 (β-secretase)

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Testing a Flexible-receptor Docking Algorithm in a Model Binding Site

inferredcites →https://doi.org/10.1016/j.jmb.2004.08.018openalex-snapshot

Apo and Inhibitor Complex Structures of BACE (β-secretase)

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Human recombinant beta-secretase immobilized enzyme reactor for fast hits’ selection and characterization from a virtual screening library

inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot

Ligand docking to proteins with discrete side-chain flexibility

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Accommodating Protein Flexibility in Computational Drug Design,

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Structural Locations and Functional Roles of New Subsites S5, S6, and S7 in Memapsin 2 (β-Secretase),

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An Inhibitor Binding Pocket Distinct from the Catalytic Active Site on Human β-APP Cleaving Enzyme

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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening

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Design, Synthesis and X-ray Structure of Protein−Ligand Complexes: Important Insight into Selectivity of Memapsin 2 (β-Secretase) Inhibitors

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Tandem Application of Virtual Screening and NMR Experiments in the Discovery of Brand New DNA Quadruplex Groove Binders

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Secretase Targets for Alzheimer's Disease: Identification and Therapeutic Potential

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Effect of Detergent on “Promiscuous” Inhibitors

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Structure-Based Design of Potent and Selective Cell-Permeable Inhibitors of Human β-Secretase (BACE-1)

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Identification of a Small Molecule Nonpeptide Active Site β-Secretase Inhibitor That Displays a Nontraditional Binding Mode for Aspartyl Proteases

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Soft Docking and Multiple Receptor Conformations in Virtual Screening

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2-Amino-3,4-dihydroquinazolines as Inhibitors of BACE-1 (β-Site APP Cleaving Enzyme): Use of Structure Based Design to Convert a Micromolar Hit into a Nanomolar Lead

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Structure-Based Virtual Screening and Biological Evaluation of Mycobacterium tuberculosis Adenosine 5′-Phosphosulfate Reductase Inhibitors

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Pursuing Aldose Reductase Inhibitors through in Situ Cross-Docking and Similarity-Based Virtual Screening

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Implications of protein flexibility for drug discovery

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A Combinatorial Approach to Protein Docking with Flexible Side Chains

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Computation of the binding of fully flexible peptides to proteins with flexible side chains

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Developing β‐secretase inhibitors for treatment of Alzheimer’s disease

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A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics

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Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor

inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot

Molecular Recognition and Docking Algorithms

inferredcites →https://doi.org/10.1517/17460441.2010.484460openalex-snapshot

Virtual screening with AutoDock: theory and practice

inferredcites →https://doi.org/10.2174/1381612023394232openalex-snapshot

Protein Flexibility is an Important Component of Structure-Based Drug Discovery

inferredcites →https://doi.org/10.2174/1381612033454595openalex-snapshot

Conformational Flexibility Models for the Receptor in Structure Based Drug Design

inferredcites →https://doi.org/10.2174/138161211796355056openalex-snapshot

Molecular Recognition in the Case of Flexible Targets

What points at this work

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

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An Integrated Approach for Fragment‐Based Lead Discovery: Virtual, NMR, and High‐Throughput Screening Combined with Structure‐Guided Design. Application to the Aspartyl Protease Renin.

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Structure‐Based Virtual Screening and Biological Characterization of Novel BACE‐1 and Amyloid‐β Aggregation Inhibitors

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(How to) Profit from Molecular Dynamics-based Ensemble Docking

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Sulfonamido, amido heterocyclic adducts of tetrazole derivatives as BACE1 inhibitors: in silico exploration

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Use of molecular docking computational tools in drug discovery

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Analysis of L-DOPA and droxidopa binding to human β2-adrenergic receptor

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A stereoselective approach to peptidomimetic BACE1 inhibitors

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Alzheimer's disease drug development based on Computer-Aided Drug Design

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Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations

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New insights in the structure-activity relationships of 2-phenylamino-substituted benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors

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Protein flexibility oriented virtual screening strategy for JAK2 inhibitors

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Lead Discovery of SARS-CoV-2 Main Protease Inhibitors through Covalent Docking-Based Virtual Screening

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Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein–Protein Interactions

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SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles

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The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening

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Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange

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DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites

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Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility

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Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

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Combined strategies in structure-based virtual screening

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Energy penalties enhance flexible receptor docking in a model cavity

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High-Order Perturbation Theory Models of Drug-Target Interactomes for Proteins Expressed on Networks of Hippocampus Brain Region of Alzheimer Disease Patients

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Search for β2 Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations

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