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Comparative evaluation of eight docking tools for docking and virtual screening accuracy
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Flexible protein–ligand docking by global energy optimization in internal coordinates
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Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
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Flexible docking using tabu search and an empirical estimate of binding affinity
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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High throughput docking for library design and library prioritization
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
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Selection criteria for drug‐like compounds
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Automatic identification and representation of protein binding sites for molecular docking
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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ConsDock: A new program for the consensus analysis of protein–ligand interactions
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A new test set for validating predictions of protein–ligand interaction
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Improved protein–ligand docking using GOLD
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Knowledge-based scoring function to predict protein-ligand interactions
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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
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A geometric approach to macromolecule-ligand interactions
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Consensus scoring for ligand/protein interactions
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LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
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Assessing the performance of OMEGA with respect to retrieving bioactive conformations
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Detailed Analysis of Scoring Functions for Virtual Screening
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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
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Novel Dihydrofolate Reductase Inhibitors. Structure-Based versus Diversity-Based Library Design and High-Throughput Synthesis and Screening
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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QXP: Powerful, rapid computer algorithms for structure-based drug design
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Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1008128723048openalex-snapshot
Ligand-receptor docking with the Mining Minima optimizer
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
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Modified AutoDock for accurate docking of protein kinase inhibitors
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The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase
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Molecular Recognition and Docking Algorithms
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Lead Identification by Virtual Screening
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inferred← citeshttps://doi.org/10.1007/s10822-005-9033-zopenalex-snapshot
Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance
inferred← citeshttps://doi.org/10.1007/s10822-006-9037-3openalex-snapshot
Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-007-9114-2openalex-snapshot
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
inferred← citeshttps://doi.org/10.1007/s10822-007-9163-6openalex-snapshot
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
inferred← citeshttps://doi.org/10.1007/s10822-008-9169-8openalex-snapshot
Evaluating docking programs: keeping the playing field level
inferred← citeshttps://doi.org/10.1007/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-009-9266-3openalex-snapshot
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
inferred← citeshttps://doi.org/10.1007/s10822-010-9385-xopenalex-snapshot
pKa based protonation states and microspecies for protein–ligand docking
inferred← citeshttps://doi.org/10.1007/s10822-010-9394-9openalex-snapshot
Biased retrieval of chemical series in receptor-based virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-011-9539-5openalex-snapshot
Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?
inferred← citeshttps://doi.org/10.1007/s10822-013-9644-8openalex-snapshot
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
inferred← citeshttps://doi.org/10.1007/s10822-013-9689-8openalex-snapshot
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
inferred← citeshttps://doi.org/10.1007/s10822-013-9697-8openalex-snapshot
Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-015-9831-xopenalex-snapshot
Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands
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/s10822-016-9930-3openalex-snapshot
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015
inferred← citeshttps://doi.org/10.1007/s10822-017-0040-7openalex-snapshot
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR
inferred← citeshttps://doi.org/10.1007/s10822-018-0180-4openalex-snapshot
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
inferred← citeshttps://doi.org/10.1007/s10822-022-00456-3openalex-snapshot
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA
inferred← citeshttps://doi.org/10.1007/s10822-026-00923-1openalex-snapshot
AI-driven drug design: a comprehensive review
inferred← citeshttps://doi.org/10.1007/s10989-019-09830-6openalex-snapshot
A Comparative Analysis of the Molecular Interaction Techniques for In Silico Drug Design
inferred← citeshttps://doi.org/10.1007/s11030-012-9417-7openalex-snapshot
High-throughput virtual screening of phloroglucinol derivatives against HIV-reverse transcriptase
inferred← citeshttps://doi.org/10.1007/s11030-023-10686-8openalex-snapshot
A computational study to identify Sesamol derivatives as NRF2 activator for protection against drug-induced liver injury (DILI)
inferred← citeshttps://doi.org/10.1007/s11099-016-0211-0openalex-snapshot
In silico, in vitro and in vivo approach in understanding the functional relationship between ergosterol and Rubisco
inferred← citeshttps://doi.org/10.1007/s11224-021-01772-4openalex-snapshot
Molecular docking and density functional theory studies of potent 1,3-disubstituted-9H-pyrido[3,4-b]indoles antifilarial compounds
inferred← citeshttps://doi.org/10.1007/s11721-007-0006-9openalex-snapshot
An ant colony optimization approach to flexible protein–ligand docking
inferred← citeshttps://doi.org/10.1007/s12539-015-0105-zopenalex-snapshot
In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum
inferred← citeshttps://doi.org/10.1007/s12551-016-0247-1openalex-snapshot
Software for molecular docking: a review
inferred← citeshttps://doi.org/10.1007/s13213-013-0751-5openalex-snapshot
Effect of metals ions on thermostable alkaline phytase from Bacillus subtilis YCJS isolated from soybean rhizosphere soil
inferred← citeshttps://doi.org/10.1007/s40203-024-00255-8openalex-snapshot
Pharmacophore mapping, 3D QSAR, molecular docking, and ADME prediction studies of novel Benzothiazinone derivatives
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00270-4openalex-snapshot
Seven Transmembrane G Protein-Coupled Receptors: Insights for Drug Design from Structure and Modeling
inferred← citeshttps://doi.org/10.1016/b978-0-12-407865-9.00015-7openalex-snapshot
From Heptahelical Bundle to Hits from the Haystack
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12323-6openalex-snapshot
Overview of Drug Polypharmacology and Multitargeted Molecular Design
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12352-2openalex-snapshot
Molecular Docking—A Solved Problem?
inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20275-6openalex-snapshot
Rational Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1016/b978-0-12-816125-8.00006-7openalex-snapshot
Molecular Docking: A Structure-Based Approach for Drug Repurposing
inferred← citeshttps://doi.org/10.1016/b978-0-12-820472-6.00042-6openalex-snapshot
Structure-Based Virtual Screening: Theory, Challenges and Guidelines
inferred← citeshttps://doi.org/10.1016/b978-0-323-89775-4.00014-6openalex-snapshot
Molecular docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1016/b978-0-323-99917-5.00009-3openalex-snapshot
Modeling and simulation of peptides
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00016-9openalex-snapshot
Molecular docking—A solved problem?
inferred← citeshttps://doi.org/10.1016/bs.armc.2022.08.008openalex-snapshot
Can docking scoring functions guarantee success in virtual screening?
inferred← citeshttps://doi.org/10.1016/j.abb.2008.12.013openalex-snapshot
The X-ray structure of ricin A chain with a novel inhibitor
inferred← citeshttps://doi.org/10.1016/j.addr.2011.11.011openalex-snapshot
Structural modelling and dynamics of proteins for insights into drug interactions
inferred← citeshttps://doi.org/10.1016/j.arr.2025.102953openalex-snapshot
The role of in silico and in vitro models in Parkinson’s disease: Drug discovery and therapy applications
inferred← citeshttps://doi.org/10.1016/j.asoc.2014.10.008openalex-snapshot
Adaptive molecular docking method based on information entropy genetic algorithm
inferred← citeshttps://doi.org/10.1016/j.bbapap.2014.02.021openalex-snapshot
Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way
inferred← citeshttps://doi.org/10.1016/j.bbrc.2025.153168openalex-snapshot
Analytical and computational chemistry approaches for mechanistic insights into nanoparticles tumor access
inferred← citeshttps://doi.org/10.1016/j.bioorg.2013.07.004openalex-snapshot
Synthesis, anti-thymidine phosphorylase activity and molecular docking of 5-thioxo-[1,2,4]triazolo[1,5-a][1,3,5]triazin-7-ones
inferred← citeshttps://doi.org/10.1016/j.bioorg.2021.104687openalex-snapshot
Synthesis, in vitro and computational studies of novel glycosyl-1, 2, 3-1H-triazolyl methyl benzamide derivatives as potential α-glucosidase inhibitory activity
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.10.052openalex-snapshot
An evaluation of automated in silico ligand docking of amino acid ligands to Family C G-protein coupled receptors
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.09.045openalex-snapshot
Synthesis, biological evaluation, and molecular modeling investigation of chiral 2-(4-chloro-phenoxy)-3-phenyl-propanoic acid derivatives with PPARα and PPARγ agonist activity
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.09.072openalex-snapshot
Synthesis, structure–activity relationships and molecular modeling studies of new indole inhibitors of monoamine oxidases A and B
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.06.054openalex-snapshot
The marine natural-derived inhibitors of glycogen synthase kinase-3β phenylmethylene hydantoins: In vitro and in vivo activities and pharmacophore modeling
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.12.019openalex-snapshot
Design and pharmacophore modeling of biaryl methyl eugenol analogs as breast cancer invasion inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmc.2014.03.018openalex-snapshot
Preliminary investigations into triazole derived androgen receptor antagonists
inferred← citeshttps://doi.org/10.1016/j.bmc.2014.11.032openalex-snapshot
Synthesis and biological evaluation of DAPY–DPEs hybrids as non-nucleoside inhibitors of HIV-1 reverse transcriptase
inferred← citeshttps://doi.org/10.1016/j.bmc.2015.01.001openalex-snapshot
Discovery of Mer kinase inhibitors by virtual screening using Structural Protein–Ligand Interaction Fingerprints
inferred← citeshttps://doi.org/10.1016/j.bmc.2015.07.058openalex-snapshot
Galantamine derivatives with indole moiety: Docking, design, synthesis and acetylcholinesterase inhibitory activity
inferred← citeshttps://doi.org/10.1016/j.bmcl.2006.06.087openalex-snapshot
Binding mode of new (thio)hydantoin inhibitors of fatty acid amide hydrolase: Comparison with two original compounds, OL-92 and JP104
inferred← citeshttps://doi.org/10.1016/j.bmcl.2012.10.018openalex-snapshot
Impact of protein binding cavity volume (PCV) and ligand volume (LV) in rigid and flexible docking of protein–ligand complexes
inferred← citeshttps://doi.org/10.1016/j.bmcl.2014.05.099openalex-snapshot
Design, synthesis and docking study of 5-(substituted benzylidene)thiazolidine-2,4-dione derivatives as inhibitors of protein tyrosine phosphatase 1B
inferred← citeshttps://doi.org/10.1016/j.bmcl.2016.12.082openalex-snapshot
Discovery of new MurA inhibitors using induced-fit simulation and docking
inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.10.061openalex-snapshot
Potential antimicrobial agents from triazole-functionalized 2H-benzo[b][1,4]oxazin-3(4H)-ones
inferred← citeshttps://doi.org/10.1016/j.carbpol.2021.118644openalex-snapshot
Application of molecular docking in elaborating molecular mechanisms and interactions of supramolecular cyclodextrin
inferred← citeshttps://doi.org/10.1016/j.cbi.2006.12.006openalex-snapshot
Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach
inferred← citeshttps://doi.org/10.1016/j.cbi.2022.110056openalex-snapshot
A novel glycosylated indolocarbazole derivative LCS1269 effectively inhibits growth of human cancer cells in vitro and in vivo through driving of both apoptosis and senescence by inducing of DNA damage and modulating of AKT/mTOR/S6K and ERK pathways
inferred← citeshttps://doi.org/10.1016/j.cbpa.2007.08.033openalex-snapshot
Virtual screening strategies in drug discovery
inferred← citeshttps://doi.org/10.1016/j.chemosphere.2011.04.010openalex-snapshot
Insights into the structural and conformational requirements of polybrominated diphenyl ethers and metabolites as potential estrogens based on molecular docking
inferred← citeshttps://doi.org/10.1016/j.colsurfb.2015.12.020openalex-snapshot
Kinetics and mechanistic study of competitive inhibition of thymidine phosphorylase by 5-fluoruracil derivatives
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.02.008openalex-snapshot
Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.106350openalex-snapshot
Discovery of Mcl-1 inhibitors through virtual screening, molecular dynamics simulations and in vitro experiments
inferred← citeshttps://doi.org/10.1016/j.comptc.2013.11.020openalex-snapshot
AlgoGen: A tool coupling a linear-scaling quantum method with a genetic algorithm for exploring non-covalent interactions
inferred← citeshttps://doi.org/10.1016/j.coph.2009.06.001openalex-snapshot
Hit finding: towards ‘smarter’ approaches
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.06.034openalex-snapshot
Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferred← citeshttps://doi.org/10.1016/j.ejmech.2006.12.037openalex-snapshot
The consequences of scoring docked ligand conformations using free energy correlations
inferred← citeshttps://doi.org/10.1016/j.ejmech.2010.05.012openalex-snapshot
3D-QSAR studies of latrunculin-based actin polymerization inhibitors using CoMFA and CoMSIA approaches
inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.07.063openalex-snapshot
Synthesis, screening and docking of small heterocycles as Glycogen Phosphorylase inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2016.05.049openalex-snapshot
Identification of noncovalent proteasome inhibitors with high selectivity for chymotrypsin-like activity by a multistep structure-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.115074openalex-snapshot
Identification of inhibitors as drug candidates against Chagas disease
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118977openalex-snapshot
Identification of novel CLK1 inhibitors by computational fragment-based ligand design, co-crystallization, chemical synthesis and structure activity relationships
inferred← citeshttps://doi.org/10.1016/j.ejphar.2024.177141openalex-snapshot
Novel applications of metformin in the treatment of septic myocardial injury based on metabolomics and network pharmacology
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e27907openalex-snapshot
Computational investigation of turmeric phytochemicals targeting PTR1 enzyme of Leishmania species
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2017.08.047openalex-snapshot
Structural basis for Cullins and RING component inhibition: Targeting E3 ubiquitin pathway conductors for cancer therapeutics
inferred← citeshttps://doi.org/10.1016/j.jff.2015.06.016openalex-snapshot
In silico investigation of action mechanism of four novel angiotensin-I converting enzyme inhibitory peptides modified with Trp
inferred← citeshttps://doi.org/10.1016/j.jmb.2005.05.066openalex-snapshot
The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure
inferred← citeshttps://doi.org/10.1016/j.jmgm.2007.11.005openalex-snapshot
Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.009openalex-snapshot
Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.04.009openalex-snapshot
Molecular docking study of macrocycles as Fk506-binding protein inhibitors
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