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A Collective Variable for the Rapid Exploration of Protein Druggability
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Outgoing claims: the papers this work cites, builds on, or argues with.
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MCSS functionality maps for a flexible protein
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Continuum electrostatic analysis of preferred solvation sites around proteins in solution
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Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics
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Development and testing of a general amber force field
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Free energy landscape of protein folding in water: Explicit vs. implicit solvent
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Exploring protein native states and large‐scale conformational changes with a modified generalized born model
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Improved side‐chain torsion potentials for the Amber ff99SB protein force field
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Ligand docking and binding site analysis with PyMOL and Autodock/Vina
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Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
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VMD: Visual molecular dynamics
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The simultaneous measurement of nicotinamide adenine dinucleotide and related compounds by liquid chromatography/electrospray ionization tandem mass spectrometry
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Exploring the active site of phenylethanolamine N-methyltransferase with 1,2,3,4-tetrahydrobenz[h]isoquinoline inhibitors
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Carbonic anhydrase inhibitors: The X-ray crystal structure of ethoxzolamide complexed to human isoform II reveals the importance of thr200 and gln92 for obtaining tight-binding inhibitors
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Bioisosterism of urea-based GCPII inhibitors: Synthesis and structure–activity relationship studies
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Discovery of piperidin-4-yl-aminopyrimidines as HIV-1 reverse transcriptase inhibitors. N-Benzyl derivatives with broad potency against resistant mutant viruses
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Dissecting Fragment-Based Lead Discovery at the von Hippel-Lindau Protein:Hypoxia Inducible Factor 1α Protein-Protein Interface
inferredcites →https://doi.org/10.1016/j.cpc.2009.05.011openalex-snapshot
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
inferredcites →https://doi.org/10.1016/j.drudis.2010.05.015openalex-snapshot
Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2011.02.002openalex-snapshot
Fragment screening to predict druggability (ligandability) and lead discovery success
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Automatic atom type and bond type perception in molecular mechanical calculations
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Specificity Determinants in Inositol Polyphosphate Synthesis: Crystal Structure of Inositol 1,3,4-Trisphosphate 5/6-Kinase
inferredcites →https://doi.org/10.1016/s0969-2126(96)00091-3openalex-snapshot
Structure of unliganded HIV-1 reverse transcriptase at 2.7 å resolution: implications of conformational changes for polymerization and inhibition mechanisms
inferredcites →https://doi.org/10.1016/s1359-6446(03)02902-7openalex-snapshot
Rediscovering the sweet spot in drug discovery
inferredcites →https://doi.org/10.1016/s1359-6446(05)03666-4openalex-snapshot
The druggable genome: an update
inferredcites →https://doi.org/10.1021/bi602474jopenalex-snapshot
Structure of the Catalytic Domain of Human Polo-like Kinase 1 ,
inferredcites →https://doi.org/10.1021/ci200266dopenalex-snapshot
DrugPred: A Structure-Based Approach To Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set
inferredcites →https://doi.org/10.1021/ci200454vopenalex-snapshot
Combining Global and Local Measures for Structure-Based Druggability Predictions
inferredcites →https://doi.org/10.1021/ci200613bopenalex-snapshot
Development of a Rule-Based Method for the Assessment of Protein Druggability
inferredcites →https://doi.org/10.1021/ci800324mopenalex-snapshot
Identifying and Characterizing Binding Sites and Assessing Druggability
inferredcites →https://doi.org/10.1021/ct300117jopenalex-snapshot
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
inferredcites →https://doi.org/10.1021/ct5007086openalex-snapshot
Accurate Multiple Time Step in Biased Molecular Simulations
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules
inferredcites →https://doi.org/10.1021/ja1079332openalex-snapshot
Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping
inferredcites →https://doi.org/10.1021/ja906844eopenalex-snapshot
Chemical Control over Immune Recognition: A Class of Antibody-Recruiting Small Molecules That Target Prostate Cancer
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Simulated Annealing of Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA
inferredcites →https://doi.org/10.1021/jm00062a027openalex-snapshot
Bis(heteroaryl)piperazine (BHAP) reverse transcriptase inhibitors: structure-activity relationships of novel substituted indole analogs and the identification of 1-[(5-methanesulfonamido-1H-indol-2-yl)carbonyl]-4-[3-[(1-methylethyl)amino]pyridinyl]piperazinemonomethanesulfonate (U-90152S), a…
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm049131ropenalex-snapshot
Druggability Indices for Protein Targets Derived from NMR-Based Screening Data
inferredcites →https://doi.org/10.1021/jm070095gopenalex-snapshot
Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction
inferredcites →https://doi.org/10.1021/jm100574mopenalex-snapshot
Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites
inferredcites →https://doi.org/10.1021/jm5011258openalex-snapshot
Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities
inferredcites →https://doi.org/10.1021/jm800562dopenalex-snapshot
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
inferredcites →https://doi.org/10.1021/jm801385dopenalex-snapshot
Binding Site Detection and Druggability Index from First Principles
inferredcites →https://doi.org/10.1021/jm960158nopenalex-snapshot
Targeting Delavirdine/Atevirdine Resistant HIV-1: Identification of (Alkylamino)piperidine-Containing Bis(heteroaryl)piperazines as Broad Spectrum HIV-1 Reverse Transcriptase Inhibitors
inferredcites →https://doi.org/10.1021/jp961992ropenalex-snapshot
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
inferredcites →https://doi.org/10.1021/np9004882openalex-snapshot
The Lecanindoles, Nonsteroidal Progestins from the Terrestrial Fungus Verticillium lecanii 6144
inferredcites →https://doi.org/10.1038/nbt1273openalex-snapshot
Structure-based maximal affinity model predicts small-molecule druggability
inferredcites →https://doi.org/10.1038/nrd1470openalex-snapshot
Can the pharmaceutical industry reduce attrition rates?
inferredcites →https://doi.org/10.1039/c3cp54164aopenalex-snapshot
Current and emerging opportunities for molecular simulations in structure-based drug design
inferredcites →https://doi.org/10.1063/1.2408420openalex-snapshot
Canonical sampling through velocity rescaling
inferredcites →https://doi.org/10.1073/pnas.252756299openalex-snapshot
Binding of small molecules to an adaptive protein–protein interface
inferredcites →https://doi.org/10.1073/pnas.94.8.3984openalex-snapshot
Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this nonnucleoside inhibitor
inferredcites →https://doi.org/10.1074/jbc.m002740200openalex-snapshot
Hypoxia Inducible Factor-α Binding and Ubiquitylation by the von Hippel-Lindau Tumor Suppressor Protein
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
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KINETIC AND MOLECULAR MODELING OF NUCLEOSIDE AND NUCLEOTIDE INHIBITION OF MALATE DEHYDROGENASE
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Nonnucleoside Inhibitors of HIV-1 Reverse Transcriptase: Nevirapine as a Prototype Drug
inferredcites →https://doi.org/10.1093/bioinformatics/bts310openalex-snapshot
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment
inferredcites →https://doi.org/10.1107/s0567739476001873openalex-snapshot
A solution for the best rotation to relate two sets of vectors
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Structure of theBrachydanio rerioPolo-like kinase 1 (Plk1) catalytic domain in complex with an extended inhibitor targeting the adaptive pocket of the enzyme
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New Method for Fast and Accurate Binding‐site Identification and Analysis
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Structural Basis of Spirolactone Recognition by the Mineralocorticoid Receptor
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L-743, 726 (DMP-266): a novel, highly potent nonnucleoside inhibitor of the human immunodeficiency virus type 1 reverse transcriptase
inferredcites →https://doi.org/10.1186/1471-2105-10-168openalex-snapshot
Fpocket: An open source platform for ligand pocket detection
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PyEvolve: a toolkit for statistical modelling of molecular evolution
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ACPYPE - AnteChamber PYthon Parser interfacE
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Target Validation: Linking Target and Chemical Properties to Desired Product Profile
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A Structural View on Druggability
inferred← citeshttps://doi.org/10.1002/9783527806539.ch6gopenalex-snapshot
Prediction, Analysis, and Comparison of Active Sites
inferred← citeshttps://doi.org/10.1002/med.70001openalex-snapshot
The Discovery of Cryptic Pockets Increases the Druggability of “Undruggable” Proteins
inferred← citeshttps://doi.org/10.1002/wcms.1529openalex-snapshot
Rational design of allosteric modulators: Challenges and successes
inferred← citeshttps://doi.org/10.1002/wcms.1676openalex-snapshot
Ligandability and druggability assessment via machine learning
inferred← citeshttps://doi.org/10.1016/j.bpj.2021.11.2561openalex-snapshot
A cryptic pocket in Ebola VP35 allosterically controls RNA binding
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Quantitative metrics for drug–target ligandability
inferred← citeshttps://doi.org/10.1016/j.sbi.2024.102975openalex-snapshot
Computational advances in discovering cryptic pockets for drug discovery
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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00221openalex-snapshot
Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00204openalex-snapshot
Finding Druggable Sites in Proteins Using TACTICS
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00660openalex-snapshot
Cryptic Pockets Repository through Pocket Dynamics Tracking and Metadynamics on Essential Dynamics Space: Applications to Mcl-1
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Druggability Assessment in TRAPP Using Machine Learning Approaches
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01244openalex-snapshot
PathGennie: Rapid Generation of Rare Event Pathways via Direction-Guided Adaptive Sampling Using Ultrashort Monitored Trajectories
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00263openalex-snapshot
Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH
inferred← citeshttps://doi.org/10.1021/acs.jpca.5c04728openalex-snapshot
Discovery of Inhibitors of SARS-CoV-2 Papain-like Protease Using Molecular Simulation and Markov State Model
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c00664openalex-snapshot
Exploring the Application of SiteMap and Site Finder for Focused Cryptic Pocket Identification
inferred← citeshttps://doi.org/10.1021/ci5006004openalex-snapshot
PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties
inferred← citeshttps://doi.org/10.1021/jacs.6b05425openalex-snapshot
Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations
inferred← citeshttps://doi.org/10.1021/jacs.6c05778openalex-snapshot
Enhanced Sampling and Ligandability Assessment to Expand the Repertoire of Potentially Druggable Cryptic Pockets
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Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators
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An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge
inferred← citeshttps://doi.org/10.1039/d5cc06159hopenalex-snapshot
Computational strategies for allosteric drug discovery: from cryptic pocket detection to rational design
inferred← citeshttps://doi.org/10.1088/0953-8984/28/34/344007openalex-snapshot
Exploring the role of water in molecular recognition: predicting protein ligandability using a combinatorial search of surface hydration sites
inferred← citeshttps://doi.org/10.1137/25m177093xopenalex-snapshot
Learning Collective Variables That Reproduce Transition Rates
inferred← citeshttps://doi.org/10.15406/mojpb.2017.05.00157openalex-snapshot
Intrinsically Disordered Proteins as Drug Targets
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A Virtual Reality Ensemble Molecular Dynamics Workflow to Study Complex Conformational Changes in Proteins
inferred← citeshttps://doi.org/10.3390/ijms231911265openalex-snapshot
Discovery of the Cryptic Sites of SARS-CoV-2 Papain-like Protease and Analysis of Its Druggability
inferred← citeshttps://doi.org/10.3390/targets2040025openalex-snapshot
Repurposing FDA-Approved Drugs Against Potential Drug Targets Involved in Brain Inflammation Contributing to Alzheimer’s Disease
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A Structure-Based Allosteric Modulator Design Paradigm
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Modulateurs synthétiques de la kallikréine 6, protéase à sérine impliquée dans les maladies neurodégénératives : identification, mécanisme d’action et validation de concept
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Etude de la structure et la dynamique de Mcl-1 : application en cancérologie
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