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Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Enhancing Hit Discovery in Virtual Screening through Absolute Protein–Ligand Binding Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00516openalex-snapshot
PheSA: An Open-Source Tool for Pharmacophore-Enhanced Shape Alignment
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01225openalex-snapshot
ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01322openalex-snapshot
ROSHAMBO2: Accelerating Molecular Alignment for Large Chemical Libraries with GPU Optimization and Algorithmic Advances
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01335openalex-snapshot
Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02202openalex-snapshot
Identification of Potential Multitarget Directed Ligands for Alzheimer’s Disease by Coupling Virtual Screening and Experimental Validation
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00216openalex-snapshot
Development and Validation of Molecular Overlays Derived from Three-Dimensional Hydrophobic Similarity with PharmScreen
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00020openalex-snapshot
BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00779openalex-snapshot
Virtual Screening in the Cloud: How Big Is Big Enough?
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01118openalex-snapshot
Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00136openalex-snapshot
Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00280openalex-snapshot
Efficient Generation of Conformer Ensembles Using Internal Coordinates and a Generative Directional Graph Convolution Neural Network
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b01756openalex-snapshot
Interactive and Versatile Navigation of Structural Databases
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c02642openalex-snapshot
Accurate Prediction of Core-Hopping Transformations Using Molecular Dynamics-Derived Conformational Ensembles: Application to the Discovery of Novel P2X3 Antagonists
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.jmedchem.9b00394openalex-snapshot
Virtual Screening Approach and Investigation of Structure–Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01324openalex-snapshot
Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02083openalex-snapshot
Hybrid Virtual Screening Approach to Predict Novel Natural Compounds against HIV-1 CCR5
inferred← citeshttps://doi.org/10.1021/acsbiomedchemau.3c00046openalex-snapshot
Shape-Based Virtual Screening of a Billion-Compound Library Identifies Mycobacterial Lipoamide Dehydrogenase Inhibitors
inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00627openalex-snapshot
Recent Advances in Virtual Screening for Cholinesterase Inhibitors
inferred← citeshttps://doi.org/10.1021/acschemneuro.1c00430openalex-snapshot
Identification of a Chlorogenic Ester as a Monoamine Oxidase (MAO-B) Inhibitor by Integrating “Traditional and Machine Learning” Virtual Screening and In Vitro as well as In Vivo Validation: A Lead against Neurodegenerative Disorders?
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.1c00662openalex-snapshot
Contemporary Computational Applications and Tools in Drug Discovery
inferred← citeshttps://doi.org/10.1021/ci200617dopenalex-snapshot
Ligand-Based Virtual Screening Approach Using a New Scoring Function
inferred← citeshttps://doi.org/10.1021/ci300030uopenalex-snapshot
Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
inferred← citeshttps://doi.org/10.1021/ci300463gopenalex-snapshot
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking
inferred← citeshttps://doi.org/10.1021/ci300601qopenalex-snapshot
Enhancing Molecular Shape Comparison by Weighted Gaussian Functions
inferred← citeshttps://doi.org/10.1021/ci400004eopenalex-snapshot
X-ray Crystallographic Structures as a Source of Ligand Alignment in 3D-QSAR
inferred← citeshttps://doi.org/10.1021/ci4000147openalex-snapshot
Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement
inferred← citeshttps://doi.org/10.1021/ci400025fopenalex-snapshot
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
inferred← citeshttps://doi.org/10.1021/ci400139jopenalex-snapshot
SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites
inferred← citeshttps://doi.org/10.1021/ci4005496openalex-snapshot
SABRE: Ligand/Structure-Based Virtual Screening Approach Using Consensus Molecular-Shape Pattern Recognition
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/ci5004619openalex-snapshot
Combining Ligand- and Structure-Based Approaches for the Discovery of New Inhibitors of the EPHA2–ephrin-A1 Interaction
inferred← citeshttps://doi.org/10.1021/ct500189sopenalex-snapshot
Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods
inferred← citeshttps://doi.org/10.1021/jm2010332openalex-snapshot
Rational Approaches to Improving Selectivity in Drug Design
inferred← citeshttps://doi.org/10.1021/jm3002718openalex-snapshot
Discovery and Optimization of 1,3,4-Trisubstituted-pyrazolone Derivatives as Novel, Potent, and Nonsteroidal Farnesoid X Receptor (FXR) Selective Antagonists
inferred← citeshttps://doi.org/10.1021/mp3006193openalex-snapshot
Physicochemical and DMPK In Silico Models: Facilitating Their Use by Medicinal Chemists
inferred← citeshttps://doi.org/10.1038/s41401-025-01571-1openalex-snapshot
Discovery of novel GluN1/GluN3A NMDA receptor inhibitors using a deep learning-based method
inferred← citeshttps://doi.org/10.1038/s41598-018-37908-6openalex-snapshot
OptiPharm: An evolutionary algorithm to compare shape similarity
inferred← citeshttps://doi.org/10.1038/s41598-020-65446-7openalex-snapshot
Structural dynamic studies on identification of EGCG analogues for the inhibition of Human Papillomavirus E7
inferred← citeshttps://doi.org/10.1038/s41598-023-49835-2openalex-snapshot
Unveiling the molecular basis of lobeline's allosteric regulation of NMDAR: insights from molecular modeling
inferred← citeshttps://doi.org/10.1038/s41598-025-85868-5openalex-snapshot
Exploring novel and potent glycogen synthase kinase-3β inhibitors through systematic drug designing approach
inferred← citeshttps://doi.org/10.1038/s42003-019-0384-8openalex-snapshot
Computational modeling of the olfactory receptor Olfr73 suggests a molecular basis for low potency of olfactory receptor-activating compounds
inferred← citeshttps://doi.org/10.1038/s42004-024-01352-7openalex-snapshot
Enabling systemic identification and functionality profiling for Cdc42 homeostatic modulators
inferred← citeshttps://doi.org/10.1038/s42256-024-00849-zopenalex-snapshot
Generic protein–ligand interaction scoring by integrating physical prior knowledge and data augmentation modelling
inferred← citeshttps://doi.org/10.1038/s42256-026-01250-8openalex-snapshot
Bridging three-dimensional molecular structures and artificial intelligence with a conformation description language
inferred← citeshttps://doi.org/10.1038/s44386-025-00017-2openalex-snapshot
Recent advances in molecular representation methods and their applications in scaffold hopping
inferred← citeshttps://doi.org/10.1039/c8ra08915aopenalex-snapshot
LSA: a local-weighted structural alignment tool for pharmaceutical virtual screening
inferred← citeshttps://doi.org/10.1039/d3ra05942aopenalex-snapshot
Bioactivity of dihydropyrimidinone derivatives as inhibitors of cyclooxygenase-2 (COX-2): an in silico approach
inferred← citeshttps://doi.org/10.1039/d4cb00272eopenalex-snapshot
The evolution and application of RNA-focused small molecule libraries
inferred← citeshttps://doi.org/10.1039/d5cp00708aopenalex-snapshot
Spatial and electronic features driving SGLT1/2 selectivity: a combined molecular dynamics and quantum mechanics study
inferred← citeshttps://doi.org/10.1039/d6dd00025hopenalex-snapshot
Generative virtual screening: from search to generate and back
inferred← citeshttps://doi.org/10.1073/pnas.2112621118openalex-snapshot
Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes
inferred← citeshttps://doi.org/10.1080/07391102.2012.732341openalex-snapshot
A novel and efficient ligand-based virtual screening approach using the HWZ scoring function and an enhanced shape-density model
inferred← citeshttps://doi.org/10.1080/07391102.2015.1119732openalex-snapshot
A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors
inferred← citeshttps://doi.org/10.1080/07391102.2018.1426046openalex-snapshot
In silico approaches to evaluate the molecular properties of organophosphate compounds to inhibit acetylcholinesterase activity in housefly
inferred← citeshttps://doi.org/10.1080/07391102.2018.1429315openalex-snapshot
In-silico screening and validation of high-affinity tetra-peptide inhibitor of Leishmania donovani O-acetyl serine sulfhydrylase (OASS)
inferred← citeshttps://doi.org/10.1080/07391102.2019.1615002openalex-snapshot
Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds
inferred← citeshttps://doi.org/10.1080/07391102.2020.1714480openalex-snapshot
In silico identification of hydantoin derivatives: a novel natural prolyl hydroxylase inhibitor
inferred← citeshttps://doi.org/10.1080/07391102.2020.1749130openalex-snapshot
Virtual screening by 2-D fingerprints, shape and docking for discovering new chemotypes of activator protein-1 inhibitors
inferred← citeshttps://doi.org/10.1080/07391102.2020.1750485openalex-snapshot
Pharmacophore- based virtual screening, 3D- QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors
inferred← citeshttps://doi.org/10.1080/07391102.2020.1775121openalex-snapshot
Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining
inferred← citeshttps://doi.org/10.1080/07391102.2020.1847195openalex-snapshot
Pharmacophore based virtual screening, molecular docking and molecular dynamic simulation studies for finding ROS1 kinase inhibitors as potential drug molecules
inferred← citeshttps://doi.org/10.1080/07391102.2022.2159532openalex-snapshot
Comprehensive screening of marine metabolites against class B1 metallo-β-lactamases of Klebsiella pneumoniae using two-pronged in silico approach
inferred← citeshttps://doi.org/10.1080/07391102.2022.2159876openalex-snapshot
Pharmacophore based virtual screening & molecular docking approach for identification of mycobacterial membrane protein large 3 (MmpL3) inhibitors
inferred← citeshttps://doi.org/10.1080/07391102.2023.2266502openalex-snapshot
Identification of novel curcumin derivatives against pancreatic cancer: a comprehensive approach integrating 3D-QSAR pharmacophore modeling, virtual screening, and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/07391102.2024.2308773openalex-snapshot
A discovery of potent kaempferol derivatives as multi-target medicines against diabetes as well as bacterial infections: an in silico approach
inferred← citeshttps://doi.org/10.1080/07391102.2025.2609702openalex-snapshot
Investigation of 3D structural specificities between neurotransmitters and receptors using the TSR-based computational method
inferred← citeshttps://doi.org/10.1080/10799893.2019.1638401openalex-snapshot
Discovery of human autophagy initiation kinase ULK1 inhibitors by multi-directionalin silicoscreening strategies
inferred← citeshttps://doi.org/10.1080/14756366.2024.2440861openalex-snapshot
Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches
inferred← citeshttps://doi.org/10.1080/14756366.2025.2546591openalex-snapshot
Discovery of a brain penetrant SGK1 inhibitor using a ligand- and structure-based virtual screening methodology
inferred← citeshttps://doi.org/10.1088/2632-2153/acefa7openalex-snapshot
Molecular machine learning with conformer ensembles
inferred← citeshttps://doi.org/10.1093/bib/bbab231openalex-snapshot
A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab205openalex-snapshot
ZEAL: protein structure alignment based on shape similarity
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae105openalex-snapshot
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt540openalex-snapshot
Shaping the interaction landscape of bioactive molecules
inferred← citeshttps://doi.org/10.1093/nar/gku293openalex-snapshot
SwissTargetPrediction: a web server for target prediction of bioactive small molecules
inferred← citeshttps://doi.org/10.1101/2020.06.01.128181openalex-snapshot
Leveraging non-structural data to predict structures of protein–ligand complexes
inferred← citeshttps://doi.org/10.1101/2023.06.18.545464openalex-snapshot
EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentation modeling
inferred← citeshttps://doi.org/10.1101/2023.11.17.567506openalex-snapshot
Enhancing Ligand-Based Virtual Screening with 3D Shape Similarity via a Distance-Aware Transformer Model
inferred← citeshttps://doi.org/10.1101/2023.12.14.571629openalex-snapshot
Conformational Space Profile Enhances Generic Molecular Representation Learning
inferred← citeshttps://doi.org/10.1101/2025.03.18.643899openalex-snapshot
Directed Chemical Evolution via Navigating Molecular Encoding Space
inferred← citeshttps://doi.org/10.1101/2025.05.07.652440openalex-snapshot
Bridging 3D Molecular Structures and Artificial Intelligence by a Conformation Description Language
inferred← citeshttps://doi.org/10.1111/cbdd.12202openalex-snapshot
Optimization of Compound Ranking for Structure‐Based Virtual Ligand Screening Using an Established FRED –Surflex Consensus Approach
inferred← citeshttps://doi.org/10.1111/cbdd.12432openalex-snapshot
Discovery of New Non‐Steroidal F arnesoid X R eceptor Modulators Through 3 D Shape Similarity Search and Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1111/cbdd.12900openalex-snapshot
ENRI: A tool for selecting structure‐based virtual screening target conformations
inferred← citeshttps://doi.org/10.1111/cbdd.13667openalex-snapshot
Comparative QSAR model generation using pyrazole derivatives for screening Janus kinase‐1 inhibitors
inferred← citeshttps://doi.org/10.1111/cbdd.70278openalex-snapshot
New Schiff Base Derivative Triazines: Their Synthesis, Molecular Docking Studies, and Anticancer Activities in Human Lung Cancer Cells
inferred← citeshttps://doi.org/10.1111/jfbc.12955openalex-snapshot
A network pharmacology study on the triterpene saponins fromMedicago sativaL. for the treatment of Neurodegenerative diseases
inferred← citeshttps://doi.org/10.1124/jpet.113.212019openalex-snapshot
Discovery of Novel Second Mitochondria-Derived Activator of Caspase Mimetics as Selective Inhibitor of Apoptosis Protein Inhibitors
inferred← citeshttps://doi.org/10.1155/2021/6480804openalex-snapshot
3D‐QSAR‐Based Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Identification of Tubulin Inhibitors with Potential Anticancer Activity
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