On the public citation graph

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

0 signed · 65 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/prot.20088openalex-snapshot

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

inferredcites →https://doi.org/10.1007/bf00124324openalex-snapshot

A genetic algorithm for flexible molecular overlay and pharmacophore elucidation

inferredcites →https://doi.org/10.1016/j.bmcl.2005.10.032openalex-snapshot

Conformationally biased P3 amide replacements of β-secretase inhibitors

inferredcites →https://doi.org/10.1016/j.bmcl.2006.11.003openalex-snapshot

β-Secretase (BACE-1) inhibitors: Accounting for 10s loop flexibility using rigid active sites

inferredcites →https://doi.org/10.1016/j.bmcl.2006.11.090openalex-snapshot

Discovery of 2-iminobenzimidazoles as a new class of trypanothione reductase inhibitor by high-throughput screening

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

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

inferredcites →https://doi.org/10.1016/j.jmgm.2005.10.002openalex-snapshot

Linear interaction energy models for β-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms

inferredcites →https://doi.org/10.1016/s0169-409x(02)00157-6openalex-snapshot

β-Secretase (BACE) as a drug target for alzheimer’s disease

inferredcites →https://doi.org/10.1021/bi048106kopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/ci034289qopenalex-snapshot

Virtual Screening Using Protein−Ligand Docking: Avoiding Artificial Enrichment

inferredcites →https://doi.org/10.1021/ci050412xopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/jm030247hopenalex-snapshot

Human β-Secretase (BACE) and BACE Inhibitors

inferredcites →https://doi.org/10.1021/jm049388popenalex-snapshot

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

inferredcites →https://doi.org/10.1021/jm049817jopenalex-snapshot

Modeling the Protonation States of the Catalytic Aspartates in β-Secretase

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

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm060154aopenalex-snapshot

Structure-Based Design and Synthesis of Macroheterocyclic Peptidomimetic Inhibitors of the Aspartic Protease β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE)

inferredcites →https://doi.org/10.1021/jm061046ropenalex-snapshot

Discovery of Oxadiazoyl Tertiary Carbinamine Inhibitors of β-Secretase (BACE-1)

inferredcites →https://doi.org/10.1021/jm0611962openalex-snapshot

Application of Fragment Screening by X-ray Crystallography to β-Secretase

inferredcites →https://doi.org/10.1021/jm061197uopenalex-snapshot

Application of Fragment Screening by X-ray Crystallography to the Discovery of Aminopyridines as Inhibitors of β-Secretase

inferredcites →https://doi.org/10.1021/jm061242yopenalex-snapshot

Design, Synthesis, and Crystal Structure of Hydroxyethyl Secondary Amine-Based Peptidomimetic Inhibitors of Human β-Secretase

inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot

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

inferredcites →https://doi.org/10.1023/a:1008781006867openalex-snapshot

Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function

inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot

Comparative study of several algorithms for flexible ligand docking

inferredcites →https://doi.org/10.1126/science.290.5489.150openalex-snapshot

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

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

Virtual Screening in Drug Discovery

inferredcites →https://doi.org/10.2174/138161207779313560openalex-snapshot

Aspartic Proteases in Drug Discovery

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ddr.20291openalex-snapshot

Structure and modeling in the design of β‐ and γ‐secretase inhibitors

inferred← citeshttps://doi.org/10.1002/jcc.24839openalex-snapshot

Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations

inferred← citeshttps://doi.org/10.1002/prot.22883openalex-snapshot

Estimating binding affinities by docking/scoring methods using variable protonation states

inferred← citeshttps://doi.org/10.1002/wcms.18openalex-snapshot

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

inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_19openalex-snapshot

Computational Modeling of Multi-target-Directed Inhibitors Against Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1007/s00249-013-0921-1openalex-snapshot

Site-specific basicities regulate molecular recognition in receptor binding: in silico docking of thyroid hormones

inferred← citeshttps://doi.org/10.1007/s10822-013-9653-7openalex-snapshot

Effect of pH and ligand charge state on BACE-1 fragment docking performance

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.biochi.2018.06.024openalex-snapshot

G-quadruplex virtual drug screening: A review

inferred← citeshttps://doi.org/10.1016/j.bmc.2010.04.030openalex-snapshot

IKKβ inhibitors identification part II: Ligand and structure-based virtual screening

inferred← citeshttps://doi.org/10.1016/j.bmcl.2009.09.103openalex-snapshot

Discovery of novel non-peptide inhibitors of BACE-1 using virtual high-throughput screening

inferred← citeshttps://doi.org/10.1016/j.bpc.2020.106536openalex-snapshot

Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer's disease treatment

inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.04.003openalex-snapshot

Determination of the protonation state for the catalytic dyad in β-secretase when bound to hydroxyethylamine transition state analogue inhibitors: A molecular dynamics simulation study

inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.07.005openalex-snapshot

Modeling the protonation states of β-secretase binding pocket by molecular dynamics simulations and docking studies

inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot

Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies

inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00813openalex-snapshot

Binding of Inhibitors to BACE1 Affected by pH-Dependent Protonation: An Exploration from Multiple Replica Gaussian Accelerated Molecular Dynamics and MM-GBSA Calculations

inferred← citeshttps://doi.org/10.1021/acsmedchemlett.1c00435openalex-snapshot

Computer Prediction of p K a Values in Small Molecules and Proteins

inferred← citeshttps://doi.org/10.1021/ci3004094openalex-snapshot

Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints

inferred← citeshttps://doi.org/10.1021/ci400620fopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/ci800420zopenalex-snapshot

Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

inferred← citeshttps://doi.org/10.1021/ci900364wopenalex-snapshot

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

inferred← citeshttps://doi.org/10.1021/jp507971vopenalex-snapshot

Underlying Thermodynamics of pH-Dependent Allostery

inferred← citeshttps://doi.org/10.1038/s41598-019-40271-9openalex-snapshot

Hybrid approach to sieve out natural compounds against dual targets in Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1080/07391102.2016.1276477openalex-snapshot

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

inferred← citeshttps://doi.org/10.1080/07391102.2017.1337590openalex-snapshot

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

inferred← citeshttps://doi.org/10.1080/07391102.2017.1393461openalex-snapshot

Population density analysis for determining the protonation state of the catalytic dyad in BACE1-tertiary carbinamine-based inhibitor complex

inferred← citeshttps://doi.org/10.1080/1062936x.2024.2419911openalex-snapshot

Molecular mechanism underlying effect of D93 and D289 protonation states on inhibitor-BACE1 binding: exploration from multiple independent Gaussian accelerated molecular dynamics and deep learning

inferred← citeshttps://doi.org/10.1111/cbdd.12568openalex-snapshot

Tubulin Inhibitor Identification by Bioactive Conformation Alignment Pharmacophore‐Guided Virtual Screening

inferred← citeshttps://doi.org/10.1186/1471-2105-11-s7-s15openalex-snapshot

IKKβ inhibitor identification: a multi-filter driven novel scaffold

inferred← citeshttps://doi.org/10.1186/1472-6807-12-21openalex-snapshot

Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)

inferred← citeshttps://doi.org/10.1186/s13321-015-0074-6openalex-snapshot

Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization

inferred← citeshttps://doi.org/10.12691/ajmo-2-4-1openalex-snapshot

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004018openalex-snapshot

Protein-Protein Docking with Dynamic Residue Protonation States

inferred← citeshttps://doi.org/10.1371/journal.pone.0037453openalex-snapshot

pKa Modulation of the Acid/Base Catalyst within GH32 and GH68: A Role in Substrate/Inhibitor Specificity?

inferred← citeshttps://doi.org/10.1371/journal.pone.0038086openalex-snapshot

Application of Consensus Scoring and Principal Component Analysis for Virtual Screening against β-Secretase (BACE-1)

inferred← citeshttps://doi.org/10.2174/1381612811319230009openalex-snapshot

On the Active Site Protonation State in Aspartic Proteases: Implications for Drug Design

inferred← citeshttps://doi.org/10.3390/ijms21030703openalex-snapshot

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

inferred← citeshttps://doi.org/10.4155/fmc.10.6openalex-snapshot

Electrostatics in Proteins and Protein–Ligand Complexes

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.