On the public citation graph

Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design

https://doi.org/10.1021/ci200366z

0 signed · 64 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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/cmdc.200600314openalex-snapshot

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

inferredcites →https://doi.org/10.1002/jcc.20035openalex-snapshot

Development and testing of a general amber force field

inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot

ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

inferredcites →https://doi.org/10.1002/med.20132openalex-snapshot

Boom in the development of non‐peptidic β‐secretase (BACE1) inhibitors for the treatment of Alzheimer's disease

inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot

Comparing protein–ligand docking programs is difficult

inferredcites →https://doi.org/10.1002/prot.21123openalex-snapshot

Comparison of multiple Amber force fields and development of improved protein backbone parameters

inferredcites →https://doi.org/10.1002/prot.22674openalex-snapshot

On the orientation of the catalytic dyad in aspartic proteases

inferredcites →https://doi.org/10.1002/prot.22711openalex-snapshot

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

inferredcites →https://doi.org/10.1006/jmbi.1994.1052openalex-snapshot

Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

inferredcites →https://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?

inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

inferredcites →https://doi.org/10.1016/j.str.2005.06.015openalex-snapshot

Functional Plasticity in the Substrate Binding Site of β-Secretase

inferredcites →https://doi.org/10.1021/bi100637nopenalex-snapshot

Effect of the Protonation State of the Titratable Residues on the Inhibitor Affinity to BACE-1

inferredcites →https://doi.org/10.1021/ci0100144openalex-snapshot

Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches

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/ci600426eopenalex-snapshot

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

inferredcites →https://doi.org/10.1021/ci9003943openalex-snapshot

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

inferredcites →https://doi.org/10.1021/ci900407copenalex-snapshot

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

inferredcites →https://doi.org/10.1021/ct0600060openalex-snapshot

Assigning the Protonation States of the Key Aspartates in β-Secretase Using QM/MM X-ray Structure Refinement

inferredcites →https://doi.org/10.1021/j100142a004openalex-snapshot

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

inferredcites →https://doi.org/10.1021/ja0304493openalex-snapshot

Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design

inferredcites →https://doi.org/10.1021/jm010425bopenalex-snapshot

Designing Non-Peptide Peptidomimetics in the 21st Century: Inhibitors Targeting Conformational Ensembles

inferredcites →https://doi.org/10.1021/jm049133bopenalex-snapshot

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

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/jm0611962openalex-snapshot

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

inferredcites →https://doi.org/10.1021/jp992492bopenalex-snapshot

Using Locally Dense Basis Sets for the Determination of Molecular Properties

inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot

Docking and scoring in virtual screening for drug discovery: methods and applications

inferredcites →https://doi.org/10.1038/nrd2092openalex-snapshot

Targeting proteases: successes, failures and future prospects

inferredcites →https://doi.org/10.1038/nrd2896openalex-snapshot

Alzheimer's disease: strategies for disease modification

inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot

Comparison of simple potential functions for simulating liquid water

inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot

Molecular dynamics with coupling to an external bath

inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems

inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00605.xopenalex-snapshot

Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

inferredcites →https://doi.org/10.1126/science.1198668openalex-snapshot

γ-Secretase and Human Disease

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/10.1371/journal.pone.0018845openalex-snapshot

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

inferredcites →https://doi.org/10.1515/bc.2010.089openalex-snapshot

Is BACE1 a suitable therapeutic target for the treatment of Alzheimer's disease? Current strategies and future directions

inferredcites →https://doi.org/10.1517/17460441.2.8.1129openalex-snapshot

Structure-guided design of β-secretase (BACE-1) inhibitors

inferredcites →https://doi.org/10.2174/092986709788186174openalex-snapshot

Progress in the Development of Nonpeptidomimetic BACE 1 Inhibitors for Alzheimers Disease

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9783527683604.ch19openalex-snapshot

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.

inferred← citeshttps://doi.org/10.1002/cmdc.201500521openalex-snapshot

Development and Application of a Virtual Screening Protocol for the Identification of Multitarget Fragments

inferred← citeshttps://doi.org/10.1007/978-981-10-3162-5_9openalex-snapshot

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

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/j.bioorg.2021.104922openalex-snapshot

Design, synthesis, and evaluation of N-benzylpyrrolidine and 1,3,4-oxadiazole as multitargeted hybrids for the treatment of Alzheimer’s disease

inferred← citeshttps://doi.org/10.1016/j.ejps.2015.05.007openalex-snapshot

Study on the active mechanism of β-secretase inhibitors by molecular simulations

inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.10.013openalex-snapshot

Computational insights into the protonation states of catalytic dyad in BACE1–acyl guanidine based inhibitor complex

inferred← citeshttps://doi.org/10.1016/j.molstruc.2021.130618openalex-snapshot

Coumarin linked heterocyclic hybrids: A promising approach to develop multi target drugs for Alzheimer's disease

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00207openalex-snapshot

Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00518openalex-snapshot

Binding Residence Time through Scaled Molecular Dynamics: A Prospective Application to hDAAO Inhibitors

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01684openalex-snapshot

Role of Molecular Dynamics and Related Methods in Drug Discovery

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00393openalex-snapshot

BACE-1 Inhibitors: From Recent Single-Target Molecules to Multitarget Compounds for Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1021/acschemneuro.9b00430openalex-snapshot

Novel Molecular Hybrids of N-Benzylpiperidine and 1,3,4-Oxadiazole as Multitargeted Therapeutics to Treat Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1021/jm301659nopenalex-snapshot

Structure-Based Design of β-Site APP Cleaving Enzyme 1 (BACE1) Inhibitors for the Treatment of Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1080/07391102.2024.2435641openalex-snapshot

Small molecule inhibits BACE1 activity by a dual mechanism confirmed by simulations-based study

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/10.1186/s12915-023-01791-zopenalex-snapshot

From byte to bench to bedside: molecular dynamics simulations and drug discovery

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/10.2174/1570159x15666170823095628openalex-snapshot

In Silico Studies in Drug Research Against Neurodegenerative Diseases

inferred← citeshttps://doi.org/10.2174/1570159x16666180315141643openalex-snapshot

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

inferred← citeshttps://doi.org/10.3109/14756366.2014.1003928openalex-snapshot

Biological and computational evaluation of resveratrol inhibitors against Alzheimer’s disease

inferred← citeshttps://doi.org/10.3390/ijms232113098openalex-snapshot

Dual Inhibitors of AChE and BACE-1 for Reducing Aβ in Alzheimer’s Disease: From In Silico to In Vivo

inferred← citeshttps://doi.org/10.47749/t/unicamp.2016.977145openalex-snapshot

Estudo QSAR da artemisinina e derivados com atividade antimalárica

inferred← citeshttps://doi.org/10.5812/jjnpp.65048openalex-snapshot

Molecular Docking and PLIF Studies of Novel Tacrine-Naphtoquinone Hybrids Based on Multi-Target-Directed Ligand Approach for Alzheimer’s Disease

inferred← citeshttps://doi.org/10.9734/jpri/2022/v34i1a35344openalex-snapshot

In Silico Molecular Docking Analysis of the Potential role of Reticuline and Coclaurine as Anti-colorectal Cancer Alkaloids

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.