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Binding Site Detection and Druggability Index from First Principles
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
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Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics
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Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00366openalex-snapshot
Predicting “Hot” and “Warm” Spots for Fragment Binding
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c00341openalex-snapshot
Computational Cosolvent Mapping Analysis Leads to Identify Salicylic Acid Analogs as Weak Inhibitors of ST2 and IL33 Binding
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c03045openalex-snapshot
Enhancing SILCS-MC via GPU Acceleration and Ligand Conformational Optimization with Genetic and Parallel Tempering Algorithms
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b03515openalex-snapshot
Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b02756openalex-snapshot
ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1021/acs.jpclett.6b01525openalex-snapshot
Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design
inferred← citeshttps://doi.org/10.1021/acs.orglett.7b02319openalex-snapshot
Concise Synthesis of Tetrazole Macrocycle
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.1c00068openalex-snapshot
Mining for Ligandable Cavities in RNA
inferred← citeshttps://doi.org/10.1021/ci100312topenalex-snapshot
Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank
inferred← citeshttps://doi.org/10.1021/ci100462topenalex-snapshot
Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations
inferred← citeshttps://doi.org/10.1021/ci200194wopenalex-snapshot
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies
inferred← citeshttps://doi.org/10.1021/ci300430vopenalex-snapshot
Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data
inferred← citeshttps://doi.org/10.1021/ci4003409openalex-snapshot
Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules
inferred← citeshttps://doi.org/10.1021/ci4003602openalex-snapshot
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity
inferred← citeshttps://doi.org/10.1021/ci400741uopenalex-snapshot
Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations
inferred← citeshttps://doi.org/10.1021/ci400750xopenalex-snapshot
Computational Method To Identify Druggable Binding Sites That Target Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/ci500215xopenalex-snapshot
The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/ct200560wopenalex-snapshot
Characterization of the Ligand Receptor Encounter Complex and Its Potential for in Silico Kinetics-Based Drug Development
inferred← citeshttps://doi.org/10.1021/ct300117jopenalex-snapshot
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
inferred← citeshttps://doi.org/10.1021/ct400361kopenalex-snapshot
Mechanism and Kinetics of Acetyl-Lysine Binding to Bromodomains
inferred← citeshttps://doi.org/10.1021/ct400967mopenalex-snapshot
Heterogeneous Hydration of p53/MDM2 Complex
inferred← citeshttps://doi.org/10.1021/ct500182zopenalex-snapshot
Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/ct500867uopenalex-snapshot
Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach
inferred← citeshttps://doi.org/10.1021/ct5010577openalex-snapshot
The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1021/ct501072topenalex-snapshot
A Collective Variable for the Rapid Exploration of Protein Druggability
inferred← citeshttps://doi.org/10.1021/ja1079332openalex-snapshot
Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping
inferred← citeshttps://doi.org/10.1021/ja905029topenalex-snapshot
Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design
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/jm100574mopenalex-snapshot
Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites
inferred← citeshttps://doi.org/10.1021/jm3011977openalex-snapshot
Scaling the Druggability Landscape of Human Bromodomains, a New Class of Drug Targets
inferred← citeshttps://doi.org/10.1021/jm5010418openalex-snapshot
Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites
inferred← citeshttps://doi.org/10.1021/jp2015758openalex-snapshot
Functionality Mapping on Internal Surfaces of Multidrug Transporter AcrB Based on Molecular Theory of Solvation: Implications for Drug Efflux Pathway
inferred← citeshttps://doi.org/10.1021/ml100026aopenalex-snapshot
Computational Analysis of Protein Hotspots
inferred← citeshttps://doi.org/10.1021/ml100276bopenalex-snapshot
Hydrophobic Binding Hot Spots of Bcl-xL Protein−Protein Interfaces by Cosolvent Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1021/ml200301wopenalex-snapshot
Analysis of Flexibility and Hotspots in Bcl-xL and Mcl-1 Proteins for the Design of Selective Small-Molecule Inhibitors
inferred← citeshttps://doi.org/10.1038/nprot.2015.043openalex-snapshot
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
inferred← citeshttps://doi.org/10.1038/nrc2980openalex-snapshot
Inside the human cancer tyrosine phosphatome
inferred← citeshttps://doi.org/10.1038/psp.2013.66openalex-snapshot
Identifying Druggable Targets by Protein Microenvironments Matching: Application to Transcription Factors
inferred← citeshttps://doi.org/10.1038/s41598-019-51977-1openalex-snapshot
Inhibition of translation termination by small molecules targeting ribosomal release factors
inferred← citeshttps://doi.org/10.1038/s41598-019-55394-2openalex-snapshot
Cosolvent Analysis Toolkit (CAT): a robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome
inferred← citeshttps://doi.org/10.1039/9781849735377-00302openalex-snapshot
Expanding the Target Space: Druggability Assessments
inferred← citeshttps://doi.org/10.1039/9781849735377-00319openalex-snapshot
Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules
inferred← citeshttps://doi.org/10.1039/c6nr07022aopenalex-snapshot
Protein corona composition of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles correlates strongly with the amino acid composition of the protein surface
inferred← citeshttps://doi.org/10.1039/c8md00166aopenalex-snapshot
An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge
inferred← citeshttps://doi.org/10.1039/c9sc05558dopenalex-snapshot
Fluorogenic Trp(redBODIPY) cyclopeptide targeting keratin 1 for imaging of aggressive carcinomas
inferred← citeshttps://doi.org/10.1039/d1md00192bopenalex-snapshot
New perspectives in cancer drug development: computational advances with an eye to design
inferred← citeshttps://doi.org/10.1039/d1nj04028fopenalex-snapshot
Application of site-identification by ligand competitive saturation in computer-aided drug design
inferred← citeshttps://doi.org/10.1073/pnas.1501567112openalex-snapshot
Ligand deconstruction: Why some fragment binding positions are conserved and others are not
inferred← citeshttps://doi.org/10.1080/14756366.2018.1476502openalex-snapshot
Identification of new allosteric sites and modulators of AChE through computational and experimental tools
inferred← citeshttps://doi.org/10.1080/17460441.2017.1362386openalex-snapshot
Computer-aided drug design: time to play with novel chemical matter
inferred← citeshttps://doi.org/10.1088/1742-6596/921/1/012002openalex-snapshot
Interactions between proteins and poly(ethylene-glycol) investigated using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1093/abbs/gmv100openalex-snapshot
Computational allosteric ligand binding site identification on Ras proteins
inferred← citeshttps://doi.org/10.1093/bib/bbz161openalex-snapshot
Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf156openalex-snapshot
Recent computational advances in the identification of cryptic binding sites for drug discovery
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag429openalex-snapshot
DruGUI 2.0: mapping protein druggability with probe-based molecular dynamics
inferred← citeshttps://doi.org/10.1093/bioinformatics/btr550openalex-snapshot
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
inferred← citeshttps://doi.org/10.1093/glycob/cws147openalex-snapshot
Solvent structure improves docking prediction in lectin–carbohydrate complexes
inferred← citeshttps://doi.org/10.1093/jmcb/mjz009openalex-snapshot
Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting
inferred← citeshttps://doi.org/10.1093/nar/gky1314openalex-snapshot
Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket
inferred← citeshttps://doi.org/10.1111/cbdd.12900openalex-snapshot
ENRI: A tool for selecting structure‐based virtual screening target conformations
inferred← citeshttps://doi.org/10.1142/9789814335058_0020openalex-snapshot
COMPUTATIONAL GENERATION INHIBITOR-BOUND CONFORMERS OF P38 MAP KINASE AND COMPARISON WITH EXPERIMENTS
inferred← citeshttps://doi.org/10.1177/1087057112437763openalex-snapshot
Perspectives on the Discovery of Small-Molecule Modulators for Epigenetic Processes
inferred← citeshttps://doi.org/10.1186/s13321-024-00819-yopenalex-snapshot
Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART)
inferred← citeshttps://doi.org/10.1208/s12248-012-9426-6openalex-snapshot
Pocket-Based Drug Design: Exploring Pocket Space
inferred← citeshttps://doi.org/10.1248/cpb.c21-00238openalex-snapshot
Elaboration of Non-naturally Occurring Helical Tripeptides as p53–MDM2/MDMX Interaction Inhibitors
inferred← citeshttps://doi.org/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002002openalex-snapshot
The Free Energy Landscape of Small Molecule Unbinding
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002951openalex-snapshot
Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1003741openalex-snapshot
Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004469openalex-snapshot
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
inferred← citeshttps://doi.org/10.1371/journal.pone.0069907openalex-snapshot
Analysis of the Interaction Interfaces of the N-Terminal Domain from Pseudomonas aeruginosa MutL
inferred← citeshttps://doi.org/10.1371/journal.pone.0137279openalex-snapshot
To Hit or Not to Hit, That Is the Question – Genome-wide Structure-Based Druggability Predictions for Pseudomonas aeruginosa Proteins
inferred← citeshttps://doi.org/10.1371/journal.pone.0178381openalex-snapshot
Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches
inferred← citeshttps://doi.org/10.1371/journal.pone.0188134openalex-snapshot
A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands
inferred← citeshttps://doi.org/10.1371/journal.pone.0294437openalex-snapshot
Validation of a highly sensitive HaloTag-based assay to evaluate the potency of a novel class of allosteric β-Galactosidase correctors
inferred← citeshttps://doi.org/10.1371/journal.pone.0303789openalex-snapshot
Discovery of allosteric regulators with clinical potential to stabilize alpha-L-iduronidase in mucopolysaccharidosis type I
inferred← citeshttps://doi.org/10.1517/17460441.2010.523697openalex-snapshot
In silico fragment-based drug design
inferred← citeshttps://doi.org/10.1517/17460441003713462openalex-snapshot
Tackling the challenges posed by target flexibility in drug design
inferred← citeshttps://doi.org/10.21203/rs.3.rs-29814/v1openalex-snapshot
Novel Potential Binding Sites for Selective Inhibitor Design of Human Soluble Epoxide Hydrolase
inferred← citeshttps://doi.org/10.2174/138161212802651553openalex-snapshot
Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application
inferred← citeshttps://doi.org/10.2174/13816128113199990073openalex-snapshot
Druggable Orthosteric and Allosteric Hot Spots to Target Protein-protein Interactions
inferred← citeshttps://doi.org/10.2174/1389203720666190417120758openalex-snapshot
Structure-based Druggability Assessment of Anti-virulence Targets from Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.2174/156802611794072641openalex-snapshot
Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death
inferred← citeshttps://doi.org/10.2174/156802611795429130openalex-snapshot
Rapid Analysis of Pharmacology for Infectious Diseases
inferred← citeshttps://doi.org/10.2174/1568026614666140929124445openalex-snapshot
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
inferred← citeshttps://doi.org/10.2174/1568026619666190816101948openalex-snapshot
Virtual Screening Techniques in Drug Discovery: Review and Recent Applications
inferred← citeshttps://doi.org/10.2174/1570163819666211223162829openalex-snapshot
Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix)
inferred← citeshttps://doi.org/10.26434/chemrxiv.12967655openalex-snapshot
Allosteric Regulation of SARS-CoV-2 Protease: Towards Informed Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.26434/chemrxiv.12967655.v1openalex-snapshot
Allosteric Regulation of SARS-CoV-2 Protease: Towards Informed Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.26434/chemrxiv.12967655.v2openalex-snapshot
Allosteric Regulation of SARS-CoV-2 Protease: Towards Informed Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.3109/1040841x.2013.826177openalex-snapshot
Bridging the past and the future of virology: Surface plasmon resonance as a powerful tool to investigate virus/host interactions
inferred← citeshttps://doi.org/10.32657/10356/69603openalex-snapshot
Exploiting receptor flexibility to improve the accuracy of structure-based virtual screening
inferred← citeshttps://doi.org/10.33011/livecoms.2.1.21383openalex-snapshot
AQUA-DUCT: Analysis of Molecular Dynamics Simulations of Macromolecules with the use of Molecular Probes [Article v1.0]
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