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Hybrid Structure-Based Virtual Screening Protocol for the Identification of Novel BACE1 Inhibitors

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What this work says

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

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Reviews in Computational Chemistry

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Similarity-driven flexible ligand docking

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Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation

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Improved protein–ligand docking using GOLD

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Comparing protein–ligand docking programs is difficult

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Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

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LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

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Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

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

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Automatic generation of 3D-atomic coordinates for organic molecules

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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

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Getting that hit: 3D database searching in drug discovery

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Scoring functions for protein–ligand interactions: a critical perspective

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Consensus scoring for protein–ligand interactions

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A new model for calculating atomic charges in molecules

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LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

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Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening

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LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

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Ligand Bias of Scoring Functions in Structure-Based Virtual Screening

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DREIDING: a generic force field for molecular simulations

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Detailed Analysis of Scoring Functions for Virtual Screening

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

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Comparative Evaluation of 11 Scoring Functions for Molecular Docking

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

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

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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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Comparison of Automated Docking Programs as Virtual Screening Tools

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Comparison of Shape-Matching and Docking as Virtual Screening Tools

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Benchmarking Sets for Molecular Docking

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A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes

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The potential of BACE inhibitors for Alzheimer's therapy

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Membrane-anchored aspartyl protease with Alzheimer's disease β-secretase activity

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BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

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β-Secretase Cleavage of Alzheimer's Amyloid Precursor Protein by the Transmembrane Aspartic Protease BACE

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Docking: Successes and Challenges

What points at this work

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

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Recent Advances in Computational Modeling of BACE1 Inhibitors as Anti-Alzheimer Agents

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Virtual Screening in the Search of New and Potent Anti-Alzheimer Agents

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Translating the Knowledge of Functional Dynamics Toward Designing Inhibitors of BACE1, a Key Aspartate Protease in Alzheimer’s Disease

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Exploration of structural and physicochemical requirements and search of virtual hits for aminopeptidase N inhibitors

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Novel non-peptide β-secretase inhibitors derived from structure-based virtual screening and bioassay

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Computational protein design and protein-ligand interaction studies for the improvement of organophosphorus degrading potential of Deinococcus radiodurans

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Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics

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Identification of Novel Malarial Cysteine Protease Inhibitors Using Structure-Based Virtual Screening of a Focused Cysteine Protease Inhibitor Library

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Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

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Target specific proteochemometric model development for BACE1 – protein flexibility and structural water are critical in virtual screening

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Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property

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Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads

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Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis

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Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics

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Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective

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Synthesis, in vitro Biological Evaluation and Molecular Docking Studies of Benzimidamides as Potential BACE1 Inhibitors

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The Discovery of Novel β‐Secretase Inhibitors: Pharmacophore Modeling, Virtual Screening, and Docking Studies

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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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Methods and Applications of Structure Based Pharmacophores in Drug Discovery

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Changing Paradigm from one Target one Ligand Towards Multi-target Directed Ligand Design for Key Drug Targets of Alzheimer Disease: An Important Role of In Silico Methods in Multi-target Directed Ligands Design

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Current Therapy and Computational Drug Designing Approaches for Neurodegenerative Diseases -with Focus on Alzheimer’s and Parkinson’s.

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Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies

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Computer-Aided Drug Design of β-Secretase, γ-Secretase and Anti-Tau Inhibitors for the Discovery of Novel Alzheimer’s Therapeutics

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Discovery of Novel Dual Vegfr2 and Src Inhibitors Using a Multistep Virtual Screening Approach

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