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Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
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Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
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PDB Ligand Conformational Energies Calculated Quantum-Mechanically
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Conformational Sampling of Bioactive Molecules: A Comparative Study
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Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm
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CAESAR: A New Conformer Generation Algorithm Based on Recursive Buildup and Local Rotational Symmetry Consideration
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Small Molecule Conformational Preferences Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis
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Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening
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GARD: A Generally Applicable Replacement for RMSD
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Clustering of Large Databases of Compounds: Using the MDL “Keys” as Structural Descriptors
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Total asymmetric transformation of an N-methylbenzamide.
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Symmetric fluoro‐substituted diol‐based HIV protease inhibitors
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Endocannabinoid activation of the TRPV1 ion channel is distinct from activation by capsaicin
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107873openalex-snapshot
A nonnatural peptide targeting the A-kinase anchoring function of PI3Kγ for therapeutic cAMP modulation in pulmonary cells
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.07.001openalex-snapshot
Structure based design towards the identification of novel binding sites and inhibitors for the chikungunya virus envelope proteins
inferred← citeshttps://doi.org/10.1016/j.jmgm.2026.109503openalex-snapshot
A benchmarking-informed structure-based virtual screening strategy targeting Lm-PTR1: Leveraging the Northern African natural products database
inferred← citeshttps://doi.org/10.1016/j.jsbmb.2016.05.019openalex-snapshot
The UVB1 Vitamin D analogue inhibits colorectal carcinoma progression
inferred← citeshttps://doi.org/10.1016/j.jsbmb.2019.04.007openalex-snapshot
Identification of the fungicide epoxiconazole by virtual screening and biological assessment as inhibitor of human 11β-hydroxylase and aldosterone synthase
inferred← citeshttps://doi.org/10.1016/j.lfs.2016.01.013openalex-snapshot
Evidence that diclofenac and celecoxib are thyroid hormone receptor beta antagonists
inferred← citeshttps://doi.org/10.1016/j.mce.2014.01.011openalex-snapshot
Identification of novel 11β-HSD1 inhibitors by combined ligand- and structure-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.msec.2017.03.157openalex-snapshot
Synthesis, structure elucidation and biological evaluation of triple bridged dinuclear copper(II) complexes as anticancer and antioxidant/anti-inflammatory agents
inferred← citeshttps://doi.org/10.1016/j.phytochem.2014.10.010openalex-snapshot
Accessing biological actions of Ganoderma secondary metabolites by in silico profiling
inferred← citeshttps://doi.org/10.1016/j.saa.2017.10.061openalex-snapshot
Human serum albumin binding of certain antimalarials
inferred← citeshttps://doi.org/10.1016/j.talanta.2017.01.072openalex-snapshot
Selective solid phase extraction of JWH synthetic cannabinoids by using computationally designed peptides
inferred← citeshttps://doi.org/10.1016/j.tiv.2014.08.009openalex-snapshot
Screening of bisphenol A, triclosan and paraben analogues as modulators of the glucocorticoid and androgen receptor activities
inferred← citeshttps://doi.org/10.1016/j.toxlet.2014.01.047openalex-snapshot
Molecular docking revealed potential disruptors of glucocorticoid receptor-dependent reporter gene expression
inferred← citeshttps://doi.org/10.1016/j.trac.2025.118536openalex-snapshot
Deep learning-driven screening of emerging contaminants: Innovations and technological advances
inferred← citeshttps://doi.org/10.1016/j.xphs.2020.10.052openalex-snapshot
Predicting the Permeability of Macrocycles from Conformational Sampling – Limitations of Molecular Flexibility
inferred← citeshttps://doi.org/10.1016/j.yjmcc.2016.08.003openalex-snapshot
Leoligin, the major lignan from Edelweiss, inhibits 3-hydroxy-3-methyl-glutaryl-CoA reductase and reduces cholesterol levels in ApoE −/− mice
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.013openalex-snapshot
Methods for generating and applying pharmacophore models as virtual screening filters and for bioactivity profiling
inferred← citeshttps://doi.org/10.1021/acs.cgd.4c00572openalex-snapshot
Crystal Structure Prediction of Drug Molecules in the Cloud: A Collaborative Blind Challenge Study
inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00155openalex-snapshot
A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts
inferred← citeshttps://doi.org/10.1021/acs.jced.7b00104openalex-snapshot
Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00025openalex-snapshot
Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00161openalex-snapshot
Scope of 3D Shape-Based Approaches in Predicting the Macromolecular Targets of Structurally Complex Small Molecules Including Natural Products and Macrocyclic Ligands
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00358openalex-snapshot
Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01451openalex-snapshot
Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01492openalex-snapshot
AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01540openalex-snapshot
Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00436openalex-snapshot
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00817openalex-snapshot
Auto3D: Automatic Generation of the Low-Energy 3D Structures with ANI Neural Network Potentials
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00649openalex-snapshot
CONFPASS: Fast DFT Re-Optimizations of Structures from Conformation Searches
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01309openalex-snapshot
Molecular Gas-Phase Conformational Ensembles
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00453openalex-snapshot
bbSelect – An Open-Source Tool for Performing a 3D Pharmacophore-Driven Diverse Selection of R-Groups
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01524openalex-snapshot
ConfRank: Improving GFN-FF Conformer Ranking with Pairwise Training
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00136openalex-snapshot
LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00186openalex-snapshot
Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00275openalex-snapshot
HybridDock: A Hybrid Protein–Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00504openalex-snapshot
Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00658openalex-snapshot
Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02074openalex-snapshot
MetalloGen: Automated 3D Conformer Generation for Diverse Coordination Complexes
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00614openalex-snapshot
A Comparison of Quantum and Molecular Mechanical Methods to Estimate Strain Energy in Druglike Fragments
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00615openalex-snapshot
A Novel Scaffold for Developing Specific or Broad-Spectrum Chitinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00749openalex-snapshot
The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00490openalex-snapshot
Exploring Conformer Search Workflows Using OpenBabel, Hierarchical Clustering, and Quantum Chemical Optimizations: A Workflow Study Including Oligothiophenes and Y6
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00591openalex-snapshot
Struct2Query: Structure-Guided Virtual Screening via Composite-Molecule ROCS Queries Derived from Protein Pocket Similarity
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00455openalex-snapshot
Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00618openalex-snapshot
ReFlex3D: Refined Flexible Alignment of Molecules Using Shape and Electrostatics
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00697openalex-snapshot
Knowledge-Based Conformer Generation Using the Cambridge Structural Database
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00582openalex-snapshot
Converging a Knowledge-Based Scoring Function: DrugScore2018
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00884openalex-snapshot
Virtual Screening Approach for the Identification of Hydroxamic Acids as Novel Human Ecto-5′-Nucleotidase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00503openalex-snapshot
Dissecting Molecular Principles of the Hsp90 Chaperone Regulation by Allosteric Modulators Using a Hierarchical Simulation Approach and Network Modeling of Allosteric Interactions: Conformational Selection Dictates the Diversity of Protein Responses and Ligand-Specific Functional Mechanisms
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01025openalex-snapshot
Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00449openalex-snapshot
Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00169openalex-snapshot
Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00640openalex-snapshot
Escaping Atom Types in Force Fields Using Direct Chemical Perception
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01232openalex-snapshot
Aryloxy Diester Phosphonamidate Prodrugs of Phosphoantigens (ProPAgens) as Potent Activators of Vγ9/Vδ2 T-Cell Immune Responses
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c02036openalex-snapshot
Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c00482openalex-snapshot
Unraveling the Role of Linker Design in Proteolysis Targeting Chimeras
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01884openalex-snapshot
Identification of Novel Human 15-Lipoxygenase-2 (h15-LOX-2) Inhibitors Using a Virtual Screening Approach
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b00150openalex-snapshot
DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b02008openalex-snapshot
Docking Screens for Novel Ligands Conferring New Biology
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c00445openalex-snapshot
The Logic of Chemical Optimization
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b00725openalex-snapshot
When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01393openalex-snapshot
Newly Designed Quinolinol Inhibitors Mitigate the Effects of Botulinum Neurotoxin A in Enzymatic, Cell-Based, and ex Vivo Assays
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01890openalex-snapshot
Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01897openalex-snapshot
Kinetin Riboside and Its ProTides Activate the Parkinson’s Disease Associated PTEN-Induced Putative Kinase 1 (PINK1) Independent of Mitochondrial Depolarization
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00262openalex-snapshot
Bio-Inspired Dual-Selective BCL-2/c-MYC G-Quadruplex Binders: Design, Synthesis, and Anticancer Activity of Drug-like Imidazo[2,1-i]purine Derivatives
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01809openalex-snapshot
Discovery of Highly Potent Benzimidazole Derivatives as Indoleamine 2,3-Dioxygenase-1 (IDO1) Inhibitors: From Structure-Based Virtual Screening to in Vivo Pharmacodynamic Activity
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.6b00139openalex-snapshot
Selecting the Most Appropriate NMR Experiment to Access Weak and/or Very Long-Range Heteronuclear Correlations
inferred← citeshttps://doi.org/10.1021/acs.joc.5b02321openalex-snapshot
Atropisomerization of 8-Membered Dibenzolactam: Experimental NMR and Theoretical DFT Study
inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c11152openalex-snapshot
Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis – Trans Isomerization and the Chameleonic Roles of Calcium
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c00016openalex-snapshot
Rapid Identification of Inhibitors and Prediction of Ligand Selectivity for Multiple Proteins: Application to Protein Kinases
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c01558openalex-snapshot
The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5b06703openalex-snapshot
Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive
inferred← citeshttps://doi.org/10.1021/acs.macromol.0c01896openalex-snapshot
Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly( N -vinylcaprolactam) in Aqueous Solution
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.5c01600openalex-snapshot
Conformation-Dependent Complexation Interactions for a SMARCA2 PROTAC and Cyclodextrin
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