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Evaluation of Docking Performance: Comparative Data on Docking Algorithms
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Assessing search strategies for flexible docking
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Evaluation of the CASP2 docking section
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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A new test set for validating predictions of protein–ligand interaction
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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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On the use of quantum energy surfaces in the derivation of molecular force fields
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LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
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inferredcites →https://doi.org/10.1107/s0021889883010985openalex-snapshot
Analytical molecular surface calculation
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inferred← citeshttps://doi.org/10.1007/s10822-016-9984-2openalex-snapshot
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies
inferred← citeshttps://doi.org/10.1007/s10822-018-0099-9openalex-snapshot
An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant
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/s10822-020-00318-wopenalex-snapshot
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer’s disease
inferred← citeshttps://doi.org/10.1007/s10895-016-1986-xopenalex-snapshot
Correlation Between Molecular Modelling and Spectroscopic Techniques in Investigation With DNA Binding Interaction of Ruthenium(II) Complexes
inferred← citeshttps://doi.org/10.1007/s11030-006-9039-zopenalex-snapshot
Reverse fingerprinting, similarity searching by group fusion and fingerprint bit importance
inferred← citeshttps://doi.org/10.1007/s11030-012-9405-yopenalex-snapshot
De novo design of N-(pyridin-4-ylmethyl)aniline derivatives as KDR inhibitors: 3D-QSAR, molecular fragment replacement, protein-ligand interaction fingerprint, and ADMET prediction
inferred← citeshttps://doi.org/10.1007/s11030-015-9592-4openalex-snapshot
Fragment virtual screening based on Bayesian categorization for discovering novel VEGFR-2 scaffolds
inferred← citeshttps://doi.org/10.1007/s11030-017-9750-yopenalex-snapshot
QSAR modeling and in silico design of small-molecule inhibitors targeting the interaction between E3 ligase VHL and HIF-1 $$\alpha $$ α
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/s11030-025-11456-4openalex-snapshot
Structure-guided design and DFT-based optimization of natural product-derived dual inhibitors targeting CDK-1 and PARP-1
inferred← citeshttps://doi.org/10.1007/s11164-018-3685-5openalex-snapshot
Palladium acetate-catalysed one-pot green synthesis of bis α-aminophosphonates
inferred← citeshttps://doi.org/10.1007/s11164-019-04068-9openalex-snapshot
Design, synthesis and exploration of in silico α-amylase and α-glucosidase binding studies of pyrrolidine-appended quinoline-constrained compounds
inferred← citeshttps://doi.org/10.1007/s11224-015-0610-zopenalex-snapshot
Theoretical study of binding affinity for diamidine with DNA
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/s12272-011-0906-5openalex-snapshot
A python-based docking program utilizing a receptor bound ligand shape: PythDock
inferred← citeshttps://doi.org/10.1007/s12551-016-0247-1openalex-snapshot
Software for molecular docking: a review
inferred← citeshttps://doi.org/10.1007/s13205-023-03897-1openalex-snapshot
Design, synthesis, molecular docking and pharmacological evaluation of some thiadiazole based nipecotic acid derivatives as a potential anticonvulsant and antidepressant agents
inferred← citeshttps://doi.org/10.1007/s13346-024-01611-zopenalex-snapshot
Nanocomposite alginate hydrogel loaded with propranolol hydrochloride kolliphor® based cerosomes as a repurposed platform for Methicillin-Resistant Staphylococcus aureus-(MRSA)-induced skin infection; in-vitro, ex-vivo, in-silico, and in-vivo evaluation
inferred← citeshttps://doi.org/10.1007/s13738-018-01580-4openalex-snapshot
Synthesis and exploration of in-silico and in-vitro α-glucosidase and α-amylase inhibitory activities of N-(3-acetyl-2-methyl-4-phenylquinolin-6-yl)arylamides
inferred← citeshttps://doi.org/10.1007/s13738-020-01913-2openalex-snapshot
Molecular docking studies and synthesis of a new class of chroman-4-one fused 1,3,4-thiadiazole derivatives and evaluation for their anticancer potential
inferred← citeshttps://doi.org/10.1007/s13738-026-03481-3openalex-snapshot
Emerging computational tools and advanced technologies in chemical and medical research: applications in bioinformatics, drug discovery, and precision healthcare: a review
inferred← citeshttps://doi.org/10.1007/s40995-023-01502-xopenalex-snapshot
A Comprehensive Study on the Binding of Anti-cancer Drug (Floxuridine) with Human Serum Albumin
inferred← citeshttps://doi.org/10.1016/b978-0-12-386485-7.00003-xopenalex-snapshot
Hybrid Schemes Based on Quantum Mechanics/Molecular Mechanics Simulations
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/b978-0-12-820472-6.00042-6openalex-snapshot
Structure-Based Virtual Screening: Theory, Challenges and Guidelines
inferred← citeshttps://doi.org/10.1016/b978-0-32-390257-1.00025-5openalex-snapshot
Quantum similarity description of a unique classical and quantum QSPR algorithm in molecular spaces: the connection with Boolean hypercubes, algorithmic intelligence, and Gödel's incompleteness theorems
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/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.abb.2026.110971openalex-snapshot
Natural metabolites from Tabebuia aurea reveal isoform-specific and cooperative modulation of cathepsins B and L
inferred← citeshttps://doi.org/10.1016/j.antiviral.2014.01.018openalex-snapshot
Small molecule inhibition of Epstein–Barr virus nuclear antigen-1 DNA binding activity interferes with replication and persistence of the viral genome
inferred← citeshttps://doi.org/10.1016/j.antiviral.2019.104621openalex-snapshot
Virtual screening identified compounds that bind to cyclin dependent kinase 2 and prevent herpes simplex virus type 1 replication and reactivation in neurons
inferred← citeshttps://doi.org/10.1016/j.arabjc.2020.03.009openalex-snapshot
Synthesis and pharmacological evaluation of 3-[5-(aryl-[1,3,4]oxadiazole-2-yl]-piperidine derivatives as anticonvulsant and antidepressant agents
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.biochi.2018.06.024openalex-snapshot
G-quadruplex virtual drug screening: A review
inferred← citeshttps://doi.org/10.1016/j.bioorg.2016.10.003openalex-snapshot
Design, synthesis, evaluation and molecular modelling studies of some novel 5,6-diphenyl-1,2,4-triazin-3(2H)-ones bearing five-member heterocyclic moieties as potential COX-2 inhibitors: A hybrid pharmacophore approach
inferred← citeshttps://doi.org/10.1016/j.bioorg.2017.04.019openalex-snapshot
Synthesis, biological evaluation and molecular modeling study of new (1,2,4-triazole or 1,3,4-thiadiazole)-methylthio-derivatives of quinazolin-4(3 H )-one as DHFR inhibitors
inferred← citeshttps://doi.org/10.1016/j.bioorg.2018.10.009openalex-snapshot
Design and development of novel p-aminobenzoic acid derivatives as potential cholinesterase inhibitors for the treatment of Alzheimer’s disease
inferred← citeshttps://doi.org/10.1016/j.bioorg.2019.01.001openalex-snapshot
Targeting microbial resistance: Synthesis, antibacterial evaluation, DNA binding and modeling study of new chalcone-based dithiocarbamate derivatives
inferred← citeshttps://doi.org/10.1016/j.bioorg.2021.104922openalex-snapshot
Design, synthesis, and evaluation of N-benzylpyrrolidine and 1,3,4-oxadiazole as multitargeted hybrids for the treatment of Alzheimer’s disease
inferred← citeshttps://doi.org/10.1016/j.bioorg.2022.106249openalex-snapshot
New amides derived from sclareolide as anticholinesterase agents
inferred← citeshttps://doi.org/10.1016/j.bioorg.2024.107761openalex-snapshot
Discovery of new molecular hybrid derivatives with coumarin scaffold bearing pyrazole/oxadiazole moieties: Molecular docking, POM analyses, in silico pharmacokinetics and in vitro antimicrobial evaluation with identification of potent antitumor pharmacophore sites
inferred← citeshttps://doi.org/10.1016/j.bioorg.2024.107827openalex-snapshot
Unveiling the anti-cancer potentiality of phthalimide-based Analogues targeting tubulin polymerization in MCF-7 cancerous Cells: Rational design, chemical Synthesis, and Biological-coupled Computational investigation
inferred← citeshttps://doi.org/10.1016/j.bioorg.2025.108131openalex-snapshot
Discovery of novel tris-1,2,3-triazole-based hybrids as VEGFR2 inhibitors with potent anti-proliferative and cytotoxicity through apoptosis induction
inferred← citeshttps://doi.org/10.1016/j.bioorg.2025.108906openalex-snapshot
Synthesis, in vitro and in silico evaluation of halogenated xanthone and benzophenone derivatives as antibacterial agents against acne-causing bacteria
inferred← citeshttps://doi.org/10.1016/j.biopha.2018.04.061openalex-snapshot
In vitro screening, homology modeling and molecular docking studies of some pyrazole and imidazole derivatives
inferred← citeshttps://doi.org/10.1016/j.bmc.2004.09.008openalex-snapshot
Flexible docking of pyridinone derivatives into the non-nucleoside inhibitor binding site of HIV-1 reverse transcriptase
inferred← citeshttps://doi.org/10.1016/j.bmc.2006.08.034openalex-snapshot
Synthesis and evaluation of a new series of substituted acyl(thio)urea and thiadiazolo [2,3-a] pyrimidine derivatives as potent inhibitors of influenza virus neuraminidase
inferred← citeshttps://doi.org/10.1016/j.bmc.2006.11.001openalex-snapshot
Molecular modeling of binding between amidinobenzisothiazoles, with antidegenerative activity on cartilage, and matrix metalloproteinase-3
inferred← citeshttps://doi.org/10.1016/j.bmc.2007.04.006openalex-snapshot
Explaining cyclodextrin–mycotoxin interactions using a ‘natural’ force field
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.02.049openalex-snapshot
The identification of novel PLC-γ inhibitors using virtual high throughput screening
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.03.027openalex-snapshot
Combinatorial chemistry in the agrosciences
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.05.073openalex-snapshot
Synthesis, biological evaluation and docking studies of novel benzopyranone congeners for their expected activity as anti-inflammatory, analgesic and antipyretic agents
inferred← citeshttps://doi.org/10.1016/j.bmc.2010.03.030openalex-snapshot
Design of potential reverse transcriptase inhibitor containing Isatin nucleus using molecular modeling studies
inferred← citeshttps://doi.org/10.1016/j.bmc.2011.04.027openalex-snapshot
Design, synthesis, and biological evaluation of substituted hydrazone and pyrazole derivatives as selective COX-2 inhibitors: Molecular docking study
inferred← citeshttps://doi.org/10.1016/j.bmc.2016.01.039openalex-snapshot
Heptapeptide ligands against receptor-binding sites of influenza hemagglutinin toward anti-influenza therapy
inferred← citeshttps://doi.org/10.1016/j.bmc.2019.07.001openalex-snapshot
Design, synthesis, and evaluation of novel N-(4-phenoxybenzyl)aniline derivatives targeting acetylcholinesterase, β-amyloid aggregation and oxidative stress to treat Alzheimer’s disease
inferred← citeshttps://doi.org/10.1016/j.bmcl.2013.12.026openalex-snapshot
Design of the influenza virus inhibitors targeting the PA endonuclease using 3D-QSAR modeling, side-chain hopping, and docking
inferred← citeshttps://doi.org/10.1016/j.cbi.2010.04.017openalex-snapshot
Interactions of pyridinium oximes with acetylcholinesterase
inferred← citeshttps://doi.org/10.1016/j.cbi.2023.110734openalex-snapshot
Pralidoxime-like reactivator with increased lipophilicity - Molecular modeling and in vitro study
inferred← citeshttps://doi.org/10.1016/j.cbi.2023.110735openalex-snapshot
Sustainable ionic liquids-based molecular platforms for designing acetylcholinesterase reactivators
inferred← citeshttps://doi.org/10.1016/j.cbi.2025.111515openalex-snapshot
Guanylhydrazone and semicarbazone derivatives as potential prototypes for the design of cholinesterase inhibitors against Alzheimer's disease: biological evaluation and molecular modeling studies
inferred← citeshttps://doi.org/10.1016/j.cbpa.2004.06.002openalex-snapshot
Target-biased scoring approaches and expert systems in structure-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.cbpa.2011.06.005openalex-snapshot
Large-scale integrated super-computing platform for next generation virtual drug discovery
inferred← citeshttps://doi.org/10.1016/j.cdc.2016.11.001openalex-snapshot
Molecular docking studies of dithiocarbamates compounds interactions with jack-bean urease
inferred← citeshttps://doi.org/10.1016/j.chemolab.2005.06.017openalex-snapshot
Tribe-PSO: A novel global optimization algorithm and its application in molecular docking
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.06.005openalex-snapshot
Docking techniques in pharmacology: How much promising?
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2021.107460openalex-snapshot
Phytotoxic property of metabolites isolated from Garcinia gardneriana
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.ddtec.2004.08.004openalex-snapshot
Scoring functions for protein–ligand interactions: a critical perspective
inferred← citeshttps://doi.org/10.1016/j.ejmcr.2025.100289openalex-snapshot
Novel triazole-based coumarin compounds as acetylcholinesterase inhibitors: Evidence and mechanism of 3-acetyl coumarin tethered (2-bromophenyl)-1,2,3 triazole as a potential mixed type inhibitor
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.2007.10.011openalex-snapshot
Antitumor studies – Part 2: Structure–activity relationship study for flavin analogs including investigations on their in vitro antitumor assay and docking simulation into protein tyrosine kinase
inferred← citeshttps://doi.org/10.1016/j.ejmech.2007.10.016openalex-snapshot
An efficient tool for identifying inhibitors based on 3D-QSAR and docking using feature-shape pharmacophore of biologically active conformation – A case study with CDK2/CyclinA
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.03.043openalex-snapshot
Discovery of potential new InhA direct inhibitors based on pharmacophoreand 3D-QSAR analysis followed by in silico screening
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.06.035openalex-snapshot
Design, synthesis and pharmacological screening of novel nitric oxide donors containing 1,5-diarylpyrazolin-3-one as nontoxic NSAIDs
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.07.009openalex-snapshot
Design and one-pot synthesis of α-aminophosphonates and bis(α-aminophosphonates) by iron(III) chloride and cytotoxic activity
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.10.016openalex-snapshot
Design, synthesis and docking studies of new furobenzopyranones and pyranobenzopyranones as photoreagent towards DNA and as antimicrobial agents
inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.12.025openalex-snapshot
Post-docking virtual screening of diverse binding pockets: Comparative study using DOCK, AMMOS, X-Score and FRED scoring functions
inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.05.029openalex-snapshot
The effect of PLC-γ2 inhibitors on the growth of human tumour cells
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