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S4MPLE – Sampler For Multiple Protein–Ligand Entities: Simultaneous Docking of Several Entities

https://doi.org/10.1021/ci300495r
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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<17::aid-prot3>3.0.co;2-1openalex-snapshot
The particle concept: placing discrete water molecules during protein-ligand docking predictions
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991201)37:4<512::aid-prot3>3.0.co;2-oopenalex-snapshot
MCSS functionality maps for a flexible protein
inferredcites →https://doi.org/10.1002/cmdc.200900011openalex-snapshot
Fragment‐based Identification of Hsp90 Inhibitors
inferredcites →https://doi.org/10.1002/cmdc.201000219openalex-snapshot
Discovery of a Novel Hsp90 Inhibitor by Fragment Linking
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.20634openalex-snapshot
A semiempirical free energy force field with charge‐based desolvation
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1006/jmbi.1996.0477openalex-snapshot
A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.1996.0746openalex-snapshot
Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
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/bf00124321openalex-snapshot
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
inferredcites →https://doi.org/10.1007/s10822-009-9268-1openalex-snapshot
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
inferredcites →https://doi.org/10.1007/s10822-009-9287-yopenalex-snapshot
The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
inferredcites →https://doi.org/10.1016/0010-4655(95)00041-dopenalex-snapshot
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
inferredcites →https://doi.org/10.1016/j.jmgm.2005.12.005openalex-snapshot
Automatic atom type and bond type perception in molecular mechanical calculations
inferredcites →https://doi.org/10.1016/s1359-6446(03)02831-9openalex-snapshot
A ‘Rule of Three’ for fragment-based lead discovery?
inferredcites →https://doi.org/10.1016/s1359-6446(04)03069-7openalex-snapshot
Ligand efficiency: a useful metric for lead selection
inferredcites →https://doi.org/10.1021/bi972383sopenalex-snapshot
Inhibitor and NAD+ Binding to Poly(ADP-ribose) Polymerase As Derived from Crystal Structures and Homology Modeling,
inferredcites →https://doi.org/10.1021/ci1000407openalex-snapshot
Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes
inferredcites →https://doi.org/10.1021/ci100469nopenalex-snapshot
Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach
inferredcites →https://doi.org/10.1021/ci100510mopenalex-snapshot
Molecular Docking with Ligand Attached Water Molecules
inferredcites →https://doi.org/10.1021/ci300495ropenalex-snapshot
S4MPLE – Sampler For Multiple Protein–Ligand Entities: Simultaneous Docking of Several Entities
inferredcites →https://doi.org/10.1021/ci600342eopenalex-snapshot
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints
inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot
Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci900345hopenalex-snapshot
Ligand−Protein Cross-Docking with Water Molecules
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/ja066980qopenalex-snapshot
Classification of Water Molecules in Protein Binding Sites
inferredcites →https://doi.org/10.1021/jm00067a013openalex-snapshot
Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
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/jm030331xopenalex-snapshot
Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein−Ligand Binding Interactions
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot
Modeling Water Molecules in Protein−Ligand Docking Using GOLD
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
inferredcites →https://doi.org/10.1021/jm100059dopenalex-snapshot
Fragment-Based Drug Discovery Applied to Hsp90. Discovery of Two Lead Series with High Ligand Efficiency
inferredcites →https://doi.org/10.1021/jm100060bopenalex-snapshot
Discovery of (2,4-Dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-yl]methanone (AT13387), a Novel Inhibitor of the Molecular Chaperone Hsp90 by Fragment Based Drug Design
inferredcites →https://doi.org/10.1021/jm200350gopenalex-snapshot
How Well Can Fragments Explore Accessed Chemical Space? A Case Study from Heat Shock Protein 90
inferredcites →https://doi.org/10.1021/jm200558uopenalex-snapshot
Docking Performance of Fragments and Druglike Compounds
inferredcites →https://doi.org/10.1021/jm8000373openalex-snapshot
Recent Developments in Fragment-Based Drug Discovery
inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot
Exploiting Ordered Waters in Molecular Docking
inferredcites →https://doi.org/10.1021/jm9603781openalex-snapshot
A Virtual Screening Approach Applied to the Search for Trypanothione Reductase Inhibitors
inferredcites →https://doi.org/10.1021/jp952835fopenalex-snapshot
Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
inferredcites →https://doi.org/10.1073/pnas.90.5.1942openalex-snapshot
Cooperativity in protein-folding kinetics.
inferredcites →https://doi.org/10.1111/j.1747-0285.2007.00535.xopenalex-snapshot
Discovery and Design of Novel HSP90 Inhibitors Using Multiple Fragment‐based Design Strategies
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.2174/138620711795767884openalex-snapshot
Fragment-Based Drug Design: Computational and Experimental State of the Art
inferredcites →https://doi.org/10.4155/fmc.09.141openalex-snapshot
Native Ms: An ‘Esi’ Way to Support Structure- and Fragment-Based 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/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
inferred← citeshttps://doi.org/10.1002/minf.201700036openalex-snapshot
Generative Topographic Mapping of Conformational Space
inferred← citeshttps://doi.org/10.1002/minf.201700115openalex-snapshot
Monitoring of the Conformational Space of Dipeptides by Generative Topographic Mapping
inferred← citeshttps://doi.org/10.1002/minf.201800059openalex-snapshot
Chemistry‐driven Hit‐to‐lead Optimization Guided by Structure‐based Approaches
inferred← citeshttps://doi.org/10.1007/s10822-018-0155-5openalex-snapshot
Rescoring of docking poses under Occam’s Razor: are there simpler solutions?
inferred← citeshttps://doi.org/10.1007/s10822-022-00485-yopenalex-snapshot
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
inferred← citeshttps://doi.org/10.1016/j.ejmech.2019.01.010openalex-snapshot
Pros and cons of virtual screening based on public “Big Data”: In silico mining for new bromodomain inhibitors
inferred← citeshttps://doi.org/10.1016/j.jsb.2019.04.017openalex-snapshot
Crystal structure of a xylulose 5-phosphate phosphoketolase. Insights into the substrate specificity for xylulose 5-phosphate
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2020.136656openalex-snapshot
pH affects the hormesis profiles of personal care product components on luminescence of the bacteria Vibrio qinghaiensis sp. -Q67
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00920openalex-snapshot
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00751openalex-snapshot
De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01172openalex-snapshot
“Big Data” Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c01569openalex-snapshot
Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein–Protein Interaction: A Semi-Automated “Hit Identification-to-Optimization” Approach
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b00653openalex-snapshot
Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach
inferred← citeshttps://doi.org/10.1021/ci4000163openalex-snapshot
In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE
inferred← citeshttps://doi.org/10.1021/ci4000882openalex-snapshot
Fighting Obesity with a Sugar-Based Library: Discovery of Novel MCH-1R Antagonists by a New Computational–VAST Approach for Exploration of GPCR Binding Sites
inferred← citeshttps://doi.org/10.1080/07391102.2023.2216278openalex-snapshot
Machine learning-based drug design for identification of thymidylate kinase inhibitors as a potential anti-Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1093/nar/gkae326openalex-snapshot
ChemoDOTS: a web server to design chemistry-driven focused libraries
inferred← citeshttps://doi.org/10.1186/s13321-025-01005-4openalex-snapshot
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands
inferred← citeshttps://doi.org/10.15407/dopovidi2019.09.060openalex-snapshot
Синтез та антиагрегаційна активність антагоніста αIIbβ3--рецепторів на основі 2-(4-піперазин-1-іл)-3Н-хіназолін-4-ону
inferred← citeshttps://doi.org/10.2174/1570180817999200618103328openalex-snapshot
In Silico ADMET and Docking Studies of Thiazolidinedione-acetic-acid Hybrids as Antidiabetics with Cardioprotection
inferred← citeshttps://doi.org/10.3389/fpls.2018.00097openalex-snapshot
Novel α-Tubulin Mutations Conferring Resistance to Dinitroaniline Herbicides in Lolium rigidum
inferred← citeshttps://doi.org/10.3390/molecules20058997openalex-snapshot
S4MPLE—Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking
inferred← citeshttps://doi.org/10.3390/molecules24122269openalex-snapshot
Generative Topographic Mapping of the Docking Conformational Space
inferred← citeshttps://doi.org/10.4172/2161-0444.1000158openalex-snapshot
From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists
inferred← citeshttps://doi.org/10.70675/809d695ezc74ez4dcazb0a4z03ef556d240copenalex-snapshot
Inhibitors of protein-protein interactions as innovative therapeutic strategy in oncology
inferred← citeshttps://doi.org/10.70675/c008e474z24bdz4952z9a55zd95b6931822copenalex-snapshot
Développement d'inhibiteurs d'interaction protéine-protéine ciblant les protéines à bromodomaines : implications en épigénétique et dans le développement de cancers
inferred← citeshttps://doi.org/10.70675/c587ee7az1c07z426dz875ezaaa1b3ab8c47openalex-snapshot
Chemical cartography and complex systems modeling
inferred← citeshttps://doi.org/10.70675/d5fdc018z1d3fz4af2zb794zae806588d521openalex-snapshot
Development of novel algorithms for data-driven prediction of interactions between proteins and small molecules
inferred← citeshttps://doi.org/10.70675/ff1b1b1bz4ecfz4beaz84cdzd1749249403dopenalex-snapshot
Generative topographic mapping : a powerful tool for big chemical data visualization, analysis and modeling
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