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Ligand Pose and Orientational Sampling in Molecular Docking

https://doi.org/10.1371/journal.pone.0075992

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inferred← citeshttps://doi.org/10.1007/s10822-015-9870-3openalex-snapshot

Ultrafast protein structure-based virtual screening with Panther

inferred← citeshttps://doi.org/10.1007/s10822-023-00507-3openalex-snapshot

On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R

inferred← citeshttps://doi.org/10.1007/s10822-023-00523-3openalex-snapshot

Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation

inferred← citeshttps://doi.org/10.1007/s10822-026-00855-wopenalex-snapshot

DOCKweb: a web-based GUI platform for molecular modeling with DOCK6

inferred← citeshttps://doi.org/10.1007/s11030-026-11627-xopenalex-snapshot

Benchmarking docking and ML re-scoring screening performance for KRAS G12D in pancreatic cancer

inferred← citeshttps://doi.org/10.1007/s11064-026-04727-5openalex-snapshot

Ibogalogs Activate the 5-HT2A Receptor through a Mechanism Involving Outward and Inward Movements of the Respective Transmembrane Segment TM6 and TM7

inferred← citeshttps://doi.org/10.1007/s12013-024-01540-1openalex-snapshot

Computational Drug Design Approaches for the Identification of Novel Antidiabetic Compounds from Natural Resources through Molecular Docking, ADMET, and Toxicological Studies

inferred← citeshttps://doi.org/10.1016/j.apsb.2025.07.043openalex-snapshot

CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening

inferred← citeshttps://doi.org/10.1016/j.bbrc.2019.05.031openalex-snapshot

Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism

inferred← citeshttps://doi.org/10.1016/j.bbrc.2022.01.037openalex-snapshot

Crystal structure of the plant feruloyl–coenzyme A monolignol transferase provides insights into the formation of monolignol ferulate conjugates

inferred← citeshttps://doi.org/10.1016/j.bioorg.2026.110313openalex-snapshot

Ligand-based design and synthesis of novel 3-spiro-2-oxindoline derivatives as potent VEGFR-2 inhibitors with antiproliferative activity and cell cycle arrest

inferred← citeshttps://doi.org/10.1016/j.bmc.2022.116879openalex-snapshot

Fragment hopping protocol for the design of small-molecule protein–protein interaction inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmcl.2022.128841openalex-snapshot

Development of an automated screen for Kv7.2 potassium channels and discovery of a new agonist chemotype

inferred← citeshttps://doi.org/10.1016/j.bpj.2026.04.011openalex-snapshot

Docking-based virtual screening: Past, present, and future

inferred← citeshttps://doi.org/10.1016/j.cell.2016.12.033openalex-snapshot

Crystal Structure of an LSD-Bound Human Serotonin Receptor

inferred← citeshttps://doi.org/10.1016/j.cell.2020.08.024openalex-snapshot

Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor

inferred← citeshttps://doi.org/10.1016/j.cell.2023.04.010openalex-snapshot

Structure-based discovery of conformationally selective inhibitors of the serotonin transporter

inferred← citeshttps://doi.org/10.1016/j.cell.2024.04.046openalex-snapshot

Structure-based discovery of CFTR potentiators and inhibitors

inferred← citeshttps://doi.org/10.1016/j.comtox.2019.100091openalex-snapshot

In silico site-directed mutagenesis of the Daphnia magna ecdysone receptor identifies critical amino acids for species-specific and inter-species differences in agonist binding

inferred← citeshttps://doi.org/10.1016/j.cub.2014.07.038openalex-snapshot

Actin Is Required for IFT Regulation in Chlamydomonas reinhardtii

inferred← citeshttps://doi.org/10.1016/j.drudis.2024.104137openalex-snapshot

Are protein–ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease?

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2022.113323openalex-snapshot

Evaluation of the binding performance of flavonoids to estrogen receptor alpha by Autodock, Autodock Vina and Surflex-Dock

inferred← citeshttps://doi.org/10.1016/j.ecoenv.2024.116582openalex-snapshot

Navigating the complexities of docking tools with nicotinic receptors and acetylcholine binding proteins in the realm of neonicotinoids

inferred← citeshttps://doi.org/10.1016/j.ejmech.2018.08.078openalex-snapshot

Substitution at the indole 3 position yields highly potent indolecombretastatins against human tumor cells

inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.115498openalex-snapshot

Structure-based discovery of novel cruzain inhibitors with distinct trypanocidal activity profiles

inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.116616openalex-snapshot

Discovery and characterization of small-molecule TGR5 ligands with agonistic activity

inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.117753openalex-snapshot

Docking for Smoothened antagonist chemotypes not susceptible to a vismodegib-resistance mutation

inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.117846openalex-snapshot

Water molecules in the cannabinoid receptor 2 binding site crucially impact the discovery of novel ligands

inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118997openalex-snapshot

From fragments to drugs: How AI and in silico methods accelerate fragment-to-lead optimization

inferred← citeshttps://doi.org/10.1016/j.ejphar.2026.178918openalex-snapshot

Ibogalogs and their pyridoindole homologs activate or inhibit the 5-HT2B receptor by modulating the distance between transmembrane segments TM3 and TM6 in the orthosteric site

inferred← citeshttps://doi.org/10.1016/j.jenvman.2026.131133openalex-snapshot

The hologenomic stress legacy: A framework for soil as a transgenerational memory bank of plant immunity

inferred← citeshttps://doi.org/10.1016/j.jsbmb.2023.106427openalex-snapshot

Integration of virtual screening of phytoecdysteroids as androgen receptor inhibitors by 3D-QSAR Model, CoMFA, molecular docking and ADMET analysis: An extensive and interactive machine learning

inferred← citeshttps://doi.org/10.1016/j.sbi.2025.102998openalex-snapshot

Protein ligand structure prediction: From empirical to deep learning approaches

inferred← citeshttps://doi.org/10.1016/j.str.2026.08.002openalex-snapshot

γ-glutamyl carboxylase inhibition by Anisindione

inferred← citeshttps://doi.org/10.1016/j.tifs.2022.07.010openalex-snapshot

Atherosclerosis fate in the era of tailored functional foods: Evidence-based guidelines elicited from structure- and ligand-based approaches

inferred← citeshttps://doi.org/10.1016/j.tips.2022.12.006openalex-snapshot

Targeting in silico GPCR conformations with ultra-large library screening for hit discovery

inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.11.015openalex-snapshot

Benchmarking methods and data sets for ligand enrichment assessment in virtual screening

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00598openalex-snapshot

Property-Unmatched Decoys in Docking Benchmarks

inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00368openalex-snapshot

Ligand Strain Energy in Large Library Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00695openalex-snapshot

Prioritizing Virtual Screening with Interpretable Interaction Fingerprints

inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00999openalex-snapshot

Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01170openalex-snapshot

A High-Quality Data Set of Protein–Ligand Binding Interactions Via Comparative Complex Structure Modeling

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01406openalex-snapshot

DockOpt: A Tool for Automatic Optimization of Docking Models

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01661openalex-snapshot

Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01749openalex-snapshot

Docking for Molecules That Bind in a Symmetric Stack with SymDOCK

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00311openalex-snapshot

Proximity Graph Networks: Predicting Ligand Affinity with Message Passing Neural Networks

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00461openalex-snapshot

DeltaGzip: Computing Biopolymer–Ligand Binding Affinity via Kolmogorov Complexity and Lossless Compression

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00683openalex-snapshot

Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01623openalex-snapshot

Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c02192openalex-snapshot

iScore: A ML-Based Scoring Function for De Novo Drug Discovery

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c02296openalex-snapshot

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00056openalex-snapshot

Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease

inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00559openalex-snapshot

ZINC 15 – Ligand Discovery for Everyone

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00850openalex-snapshot

Autoparty: Machine Learning-Guided Visual Inspection of Molecular Docking Results

inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01925openalex-snapshot

Protein Structural Model Selection Informed by Comparison of Predicted Ligand Binding Poses

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00034openalex-snapshot

Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01066openalex-snapshot

Modeling the Sensitivity of Large-Scale Virtual Screening to Scoring Function Accuracy, Artifacts, and Library Composition

inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00571openalex-snapshot

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00810openalex-snapshot

Efficient Exploration of Chemical Space with Docking and Deep Learning

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00345openalex-snapshot

Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir

inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01093openalex-snapshot

Hierarchical AF2RAVE for Multiconformation Virtual Screening Targeting S100 Ca2+-Binding Proteins

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c01975openalex-snapshot

Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1–Nrf2 Protein–Protein Interaction

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c02031openalex-snapshot

Structure-Based Design of a Chemical Probe Set for the 5-HT 5A Serotonin Receptor

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c02120openalex-snapshot

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c01707openalex-snapshot

Development of Fluorescent AF64394 Analogues Enables Real-Time Binding Studies for the Orphan Class A GPCR GPR3

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c03281openalex-snapshot

Small-Molecule Activators of PRMT1: Discovery, SAR Analyses, and Proapoptotic Effects in Pancreatic Cancer Cells

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00508openalex-snapshot

D2 Dopamine Receptor G Protein-Biased Partial Agonists Based on Cariprazine

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b11820openalex-snapshot

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

inferred← citeshttps://doi.org/10.1021/acscentsci.2c01190openalex-snapshot

In Silico Discovery of Small Molecule Modulators Targeting the Achilles’ Heel of SARS-CoV-2 Spike Protein

inferred← citeshttps://doi.org/10.1021/acschembio.2c00234openalex-snapshot

Structure-Based Discovery of Negative Allosteric Modulators of the Metabotropic Glutamate Receptor 5

inferred← citeshttps://doi.org/10.1021/acsomega.0c01256openalex-snapshot

β-Carboline Derivatives Tackling Malaria: Biological Evaluation and Docking Analysis

inferred← citeshttps://doi.org/10.1021/acsomega.2c05826openalex-snapshot

Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening

inferred← citeshttps://doi.org/10.1021/acsomega.5c00829openalex-snapshot

Assessing the Robustness and Scalability of Machine Learning Methods to Accelerate Ultralarge High-Throughput Docking Campaigns

inferred← citeshttps://doi.org/10.1021/acsptsci.3c00378openalex-snapshot

Discovery of Protease-Activated Receptor 4 (PAR4)-Tethered Ligand Antagonists Using Ultralarge Virtual Screening

inferred← citeshttps://doi.org/10.1021/jacs.1c08402openalex-snapshot

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

inferred← citeshttps://doi.org/10.1021/jacs.1c11900openalex-snapshot

Discovery of the Xenon–Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability

inferred← citeshttps://doi.org/10.1021/jacsau.6c00173openalex-snapshot

ProMol_Func: A Structure-Free Deep Learning Model for Virtual Screening

inferred← citeshttps://doi.org/10.1038/nature25758openalex-snapshot

Structure of the D2 dopamine receptor bound to the atypical antipsychotic drug risperidone

inferred← citeshttps://doi.org/10.1038/nchem.1954openalex-snapshot

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

inferred← citeshttps://doi.org/10.1038/s41380-024-02531-7openalex-snapshot

Pharmacological fingerprint of antipsychotic drugs at the serotonin 5-HT2A receptor

inferred← citeshttps://doi.org/10.1038/s41467-020-14722-1openalex-snapshot

Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site

inferred← citeshttps://doi.org/10.1038/s41467-023-43506-6openalex-snapshot

Docking for EP4R antagonists active against inflammatory pain

inferred← citeshttps://doi.org/10.1038/s41467-024-46096-zopenalex-snapshot

Cryo-EM structure of cell-free synthesized human histamine 2 receptor/Gs complex in nanodisc environment

inferred← citeshttps://doi.org/10.1038/s41467-025-56893-9openalex-snapshot

Virtual fragment screening for DNA repair inhibitors in vast chemical space

inferred← citeshttps://doi.org/10.1038/s41467-025-57136-7openalex-snapshot

Virtual library docking for cannabinoid-1 receptor agonists with reduced side effects

inferred← citeshttps://doi.org/10.1038/s41467-025-66845-yopenalex-snapshot

Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139

inferred← citeshttps://doi.org/10.1038/s41467-025-67147-zopenalex-snapshot

In silico docking yields small molecule negative allosteric modulators targeting the core of Frizzled 7

inferred← citeshttps://doi.org/10.1038/s41467-026-74990-1openalex-snapshot

Docking of virtual libraries identifies small-molecule agonists of neurotensin receptors with analgesic activity

inferred← citeshttps://doi.org/10.1038/s41467-026-77484-2openalex-snapshot

Structure based discovery of antipsychotic-like TAAR1 agonists

inferred← citeshttps://doi.org/10.1038/s41557-020-0467-7openalex-snapshot

FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis

inferred← citeshttps://doi.org/10.1038/s41586-019-0917-9openalex-snapshot

Ultra-large library docking for discovering new chemotypes

inferred← citeshttps://doi.org/10.1038/s41586-020-2027-0openalex-snapshot

Virtual discovery of melatonin receptor ligands to modulate circadian rhythms

inferred← citeshttps://doi.org/10.1038/s41586-022-05258-zopenalex-snapshot

Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity

inferred← citeshttps://doi.org/10.1038/s41589-024-01797-wopenalex-snapshot

The impact of library size and scale of testing on virtual screening

inferred← citeshttps://doi.org/10.1038/s41596-021-00597-zopenalex-snapshot

A practical guide to large-scale docking

inferred← citeshttps://doi.org/10.1038/s41596-023-00885-wopenalex-snapshot

A practical guide to machine-learning scoring for structure-based virtual screening

inferred← citeshttps://doi.org/10.1038/s41598-023-28785-9openalex-snapshot

AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection

inferred← citeshttps://doi.org/10.1038/s43588-025-00777-xopenalex-snapshot

Rapid traversal of vast chemical space using machine learning-guided docking screens

inferred← citeshttps://doi.org/10.1038/s44320-025-00159-5openalex-snapshot

Identification of potent high-affinity secondary nucleation inhibitors of Aβ42 aggregation from an ultra-large chemical library using deep docking

inferred← citeshttps://doi.org/10.1038/s44386-025-00019-0openalex-snapshot

AI meets physics in computational structure-based drug discovery for GPCRs

inferred← citeshttps://doi.org/10.1039/c6mb00678gopenalex-snapshot

Integrated discovery of FOXO1–DNA stabilizers from marine natural products to restore chemosensitivity to anti-EGFR-based therapy for metastatic lung cancer

inferred← citeshttps://doi.org/10.1039/c8ra03107jopenalex-snapshot

The effect of the intramolecular C–H⋯O interactions on the conformational preferences of bis-arylsulfones – 5-HT 6 receptor antagonists and beyond

inferred← citeshttps://doi.org/10.1039/d1sc05579hopenalex-snapshot

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

inferred← citeshttps://doi.org/10.1039/d5ra04875copenalex-snapshot

Integrative network pharmacology and molecular dynamics analysis of Ceiba pentandra compounds with experimental support for colorectal cancer therapy

inferred← citeshttps://doi.org/10.1039/d6dd00025hopenalex-snapshot

Generative virtual screening: from search to generate and back

inferred← citeshttps://doi.org/10.1073/pnas.1703287114openalex-snapshot

Testing inhomogeneous solvation theory in structure-based ligand discovery

inferred← citeshttps://doi.org/10.1073/pnas.1718037115openalex-snapshot

Structure-based discovery of selective positive allosteric modulators of antagonists for the M 2 muscarinic acetylcholine receptor

inferred← citeshttps://doi.org/10.1073/pnas.2106195118openalex-snapshot

Energy penalties enhance flexible receptor docking in a model cavity

inferred← citeshttps://doi.org/10.1073/pnas.2212931120openalex-snapshot

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

inferred← citeshttps://doi.org/10.1073/pnas.2421687122openalex-snapshot

Structure-based discovery of positive allosteric modulators of the A 1 adenosine receptor

inferred← citeshttps://doi.org/10.1074/jbc.m114.554790openalex-snapshot

Determinants of Substrate and Cation Transport in the Human Na+/Dicarboxylate Cotransporter NaDC3

inferred← citeshttps://doi.org/10.1074/mcp.m115.053520openalex-snapshot

Matrix Metalloproteinase 10 Degradomics in Keratinocytes and Epidermal Tissue Identifies Bioactive Substrates With Pleiotropic Functions*

inferred← citeshttps://doi.org/10.1080/07391102.2020.1747545openalex-snapshot

Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation

inferred← citeshttps://doi.org/10.1080/17460441.2024.2390511openalex-snapshot

Perspectives on current approaches to virtual screening in drug discovery

inferred← citeshttps://doi.org/10.1088/2058-9565/ae0890openalex-snapshot

Molecular docking via weighted subgraph isomorphism on quantum annealers

inferred← citeshttps://doi.org/10.1093/bib/bbaa095openalex-snapshot

The impact of compound library size on the performance of scoring functions for structure-based virtual screening

inferred← citeshttps://doi.org/10.1093/bib/bbag274openalex-snapshot

Quantum computing applications in drug discovery

inferred← citeshttps://doi.org/10.1093/bioinformatics/btu709openalex-snapshot

SEABED: Small molEcule activity scanner weB servicE baseD

inferred← citeshttps://doi.org/10.1101/2020.11.24.393405openalex-snapshot

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

inferred← citeshttps://doi.org/10.1101/2021.12.06.471449openalex-snapshot

Structure-based design of a chemical probe set for the 5-HT 5A serotonin receptor

inferred← citeshttps://doi.org/10.1101/2023.01.12.523677openalex-snapshot

Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14 N7 -methyltransferase

inferred← citeshttps://doi.org/10.1101/2023.02.27.530254openalex-snapshot

Large library docking for cannabinoid-1 receptor agonists with reduced side effects

inferred← citeshttps://doi.org/10.1101/2023.07.27.550782openalex-snapshot

Cryo-EM structure of cell-free synthesized human histamine H 2 receptor coupled to heterotrimeric G s protein in lipid nanodisc environment

inferred← citeshttps://doi.org/10.1101/2023.10.25.564029openalex-snapshot

Structure-Based Discovery of a NPFF1R Antagonist with Analgesic Activity

inferred← citeshttps://doi.org/10.1101/2023.12.27.573448openalex-snapshot

Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor

inferred← citeshttps://doi.org/10.1101/2024.04.02.587723openalex-snapshot

iScore: A ML-Based Scoring Function for de novo Drug Discovery

inferred← citeshttps://doi.org/10.1109/tpds.2022.3194916openalex-snapshot

Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight

inferred← citeshttps://doi.org/10.1124/mol.117.111153openalex-snapshot

Molecular Mechanisms for Species Differences in Organic Anion Transporter 1, OAT1: Implications for Renal Drug Toxicity

inferred← citeshttps://doi.org/10.1124/pharmrev.120.000246openalex-snapshot

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

inferred← citeshttps://doi.org/10.1124/pharmrev.121.000300openalex-snapshot

Nonantimicrobial Actions of Macrolides: Overview and Perspectives for Future Development

inferred← citeshttps://doi.org/10.1126/sciadv.abf8711openalex-snapshot

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

inferred← citeshttps://doi.org/10.1126/sciadv.adn1524openalex-snapshot

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine–associated receptor 1

inferred← citeshttps://doi.org/10.1126/sciadv.ads7187openalex-snapshot

Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning

inferred← citeshttps://doi.org/10.1126/science.aan5468openalex-snapshot

D4dopamine receptor high-resolution structures enable the discovery of selective agonists

inferred← citeshttps://doi.org/10.1126/science.aaw7611openalex-snapshot

Structural identification of a hotspot on CFTR for potentiation

inferred← citeshttps://doi.org/10.1126/science.abn7065openalex-snapshot

Structure-based discovery of nonopioid analgesics acting through the α 2A -adrenergic receptor

inferred← citeshttps://doi.org/10.1126/science.adn6354openalex-snapshot

AlphaFold2 structures guide prospective ligand discovery

inferred← citeshttps://doi.org/10.1126/science.ado1868openalex-snapshot

Large library docking identifies positive allosteric modulators of the calcium-sensing receptor

inferred← citeshttps://doi.org/10.1145/3712285.3759833openalex-snapshot

Trillion Ligands per Day: Performance-Portable Virtual Screening via Compound Database Optimization and Multi-Target Docking

inferred← citeshttps://doi.org/10.1146/annurev-biochem-030222-120000openalex-snapshot

The Art and Science of Molecular Docking

inferred← citeshttps://doi.org/10.1146/annurev-biodatasci-020222-025013openalex-snapshot

Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches

inferred← citeshttps://doi.org/10.1172/jci203162openalex-snapshot

Small molecule inhibitor of orphan GPCR dimerization improves host defense and blood pressure control in mice

inferred← citeshttps://doi.org/10.1177/10943420211001565openalex-snapshot

High-throughput virtual laboratory for drug discovery using massive datasets

inferred← citeshttps://doi.org/10.1186/s12859-019-2796-3openalex-snapshot

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics

inferred← citeshttps://doi.org/10.1186/s13321-020-00443-6openalex-snapshot

QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping

inferred← citeshttps://doi.org/10.1186/s13321-026-01287-2openalex-snapshot

DockM8: an all-in-one open-source platform for consensus virtual screening in drug design

inferred← citeshttps://doi.org/10.1186/s43094-025-00862-yopenalex-snapshot

Assessing molecular docking tools: understanding drug discovery and design

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004477openalex-snapshot

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008936openalex-snapshot

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

inferred← citeshttps://doi.org/10.1371/journal.pone.0131612openalex-snapshot

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

inferred← citeshttps://doi.org/10.1371/journal.pone.0134472openalex-snapshot

The Augmenting Effects of Desolvation and Conformational Energy Terms on the Predictions of Docking Programs against mPGES-1

inferred← citeshttps://doi.org/10.1371/journal.pone.0198476openalex-snapshot

Computational quantum chemistry, molecular docking, and ADMET predictions of imidazole alkaloids of Pilocarpus microphyllus with schistosomicidal properties

inferred← citeshttps://doi.org/10.20935/acadmolbiogen7475openalex-snapshot

Utilizing computational approaches for the prediction of alpha-PPAR inhibitors from baobab (Adansonia digitata) against non-alcoholic fatty liver disease

inferred← citeshttps://doi.org/10.2139/ssrn.5877054openalex-snapshot

Ibogalogs Activate the 5-HT2A Receptor Through a Mechanism Involving Outward and Inward Movements of the Respective Transmembrane Segment TM6 and TM7

inferred← citeshttps://doi.org/10.2147/dddt.s537065openalex-snapshot

Benchmarking the Structure-Based Virtual Screening Performance of Wild-Type and Resistant PfDHFR Using Docking and Machine Learning Re-Scoring

inferred← citeshttps://doi.org/10.2174/0929867322666150209151209openalex-snapshot

Target Based Drug Design - A Reality in Virtual Sphere

inferred← citeshttps://doi.org/10.2174/1389450119666181022153016openalex-snapshot

Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective

inferred← citeshttps://doi.org/10.2174/1568026619666181224101744openalex-snapshot

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes

inferred← citeshttps://doi.org/10.2174/1568026619666190816101948openalex-snapshot

Virtual Screening Techniques in Drug Discovery: Review and Recent Applications

inferred← citeshttps://doi.org/10.2174/1871520614666140715085907openalex-snapshot

Antineoplastic Activity of Monocrotaline Against Hepatocellular Carcinoma

inferred← citeshttps://doi.org/10.2174/9789815223019124010014openalex-snapshot

Warp and Woof of Drug Designing and Development: An In-Silico Approach

inferred← citeshttps://doi.org/10.2210/pdb6inw/pdbopenalex-snapshot

A Pericyclic Reaction enzyme

inferred← citeshttps://doi.org/10.22376/ijpbs/lpr.2021.11.2.p114-122openalex-snapshot

Lantadenes Targeting NF-ΚB in Cancer: Molecular Docking and ADMET Predictions

inferred← citeshttps://doi.org/10.24959/ophcj.21.244362openalex-snapshot

The iterative application of a large chemical space in the drug discovery process

inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-6h2c9-v2openalex-snapshot

DOCK Blaster 2.0 - Automated Optimization of Docking Models using Retrospective Docking

inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-w3x36openalex-snapshot

Rapid Traversal of Ultralarge Chemical Space using Machine Learning Guided Docking Screens

inferred← citeshttps://doi.org/10.26434/chemrxiv.13082561openalex-snapshot

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

inferred← citeshttps://doi.org/10.26434/chemrxiv.14348117openalex-snapshot

State of the Art Iterative Docking with Logistic Regression and Morgan Fingerprints

inferred← citeshttps://doi.org/10.26434/chemrxiv.14348117.v1openalex-snapshot

State of the Art Iterative Docking with Logistic Regression and Morgan Fingerprints

inferred← citeshttps://doi.org/10.29356/jmcs.v69i1.2299openalex-snapshot

UAM-Ixachi: Desktop Tool for Massive Automated Molecular Docking

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