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Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Critical evaluation of search algorithms for automated molecular docking and database screening
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Flexible docking using tabu search and an empirical estimate of binding affinity
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Efficacy and selectivity in flexible database docking
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Flexible ligand docking using conformational ensembles
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Automated docking of substrates to proteins by simulated annealing
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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How sophisticated should a scoring function be to ensure successful docking, scoring and virtual screening?
inferred← citeshttps://doi.org/10.1007/s00894-011-1066-8openalex-snapshot
Computer-aided de novo ligand design and docking/molecular dynamics study of Vitamin D receptor agonists
inferred← citeshttps://doi.org/10.1007/s00894-012-1369-4openalex-snapshot
Molecular docking studies of protein-nucleotide complexes using MOLSDOCK (mutually orthogonal Latin squares DOCK)
inferred← citeshttps://doi.org/10.1007/s00894-012-1416-1openalex-snapshot
FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols
inferred← citeshttps://doi.org/10.1007/s00894-012-1479-zopenalex-snapshot
Application of docking-based comparative intermolecular contacts analysis to validate Hsp90α docking studies and subsequent in silico screening for inhibitors
inferred← citeshttps://doi.org/10.1007/s00894-012-1586-xopenalex-snapshot
QM study and conformational analysis of an isatin Schiff base as a potential cytotoxic agent
inferred← citeshttps://doi.org/10.1007/s00894-023-05504-9openalex-snapshot
Discovery of novel S6K1 inhibitors by an ensemble-based virtual screening method and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1007/s10311-006-0065-yopenalex-snapshot
The estrogen receptor and polyphenols: molecular simulation studies of their interactions, a review
inferred← citeshttps://doi.org/10.1007/s10822-005-4788-9openalex-snapshot
In-silico Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach
inferred← citeshttps://doi.org/10.1007/s10822-005-9019-xopenalex-snapshot
Molecular shape and electrostatics in the encoding of relevant chemical information
inferred← citeshttps://doi.org/10.1007/s10822-006-9043-5openalex-snapshot
Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change
inferred← citeshttps://doi.org/10.1007/s10822-006-9067-xopenalex-snapshot
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist
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/s10822-007-9116-0openalex-snapshot
Calculations of protein-ligand binding entropy of relative and overall molecular motions
inferred← citeshttps://doi.org/10.1007/s10822-007-9150-yopenalex-snapshot
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery
inferred← citeshttps://doi.org/10.1007/s10822-007-9151-xopenalex-snapshot
Bias, reporting, and sharing: computational evaluations of docking methods
inferred← citeshttps://doi.org/10.1007/s10822-007-9152-9openalex-snapshot
Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
inferred← citeshttps://doi.org/10.1007/s10822-007-9164-5openalex-snapshot
LASSO—ligand activity by surface similarity order: a new tool for ligand based virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-007-9165-4openalex-snapshot
Can we use docking and scoring for hit-to-lead optimization?
inferred← citeshttps://doi.org/10.1007/s10822-007-9166-3openalex-snapshot
How to do an evaluation: pitfalls and traps
inferred← citeshttps://doi.org/10.1007/s10822-007-9167-2openalex-snapshot
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
inferred← citeshttps://doi.org/10.1007/s10822-008-9170-2openalex-snapshot
What do we know and when do we know it?
inferred← citeshttps://doi.org/10.1007/s10822-008-9174-yopenalex-snapshot
Customizing scoring functions for docking
inferred← citeshttps://doi.org/10.1007/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-008-9224-5openalex-snapshot
Structure-based design of Aurora A & B inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-008-9232-5openalex-snapshot
An improved adaptive genetic algorithm for protein–ligand docking
inferred← citeshttps://doi.org/10.1007/s10822-008-9249-9openalex-snapshot
VSDMIP: virtual screening data management on an integrated platform
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/s10822-010-9394-9openalex-snapshot
Biased retrieval of chemical series in receptor-based virtual screening
inferred← citeshttps://doi.org/10.1007/s10822-011-9531-0openalex-snapshot
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
inferred← citeshttps://doi.org/10.1007/s10822-011-9533-yopenalex-snapshot
Surflex-Dock: Docking benchmarks and real-world application
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/s10822-014-9740-4openalex-snapshot
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators
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/s10867-013-9299-7openalex-snapshot
Pyrazolo[3,4-d]pyrimidines as inhibitor of anti-coagulation and inflammation activities of phospholipase A 2 : insight from molecular docking studies
inferred← citeshttps://doi.org/10.1007/s10867-014-9369-5openalex-snapshot
Stabilization of Microtubules by Taxane Diterpenoids: Insight from Docking and MD simulations
inferred← citeshttps://doi.org/10.1007/s10867-022-09612-0openalex-snapshot
Fisetin decreases the duration of ictal-like discharges in mouse hippocampal slices
inferred← citeshttps://doi.org/10.1007/s11030-006-2153-0openalex-snapshot
Similarity study of serine proteases inhibitors
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/s11224-019-01414-wopenalex-snapshot
Diarylthiazole and diarylimidazole selective COX-1 inhibitor analysis through pharmacophore modeling, virtual screening, and DFT-based approaches
inferred← citeshttps://doi.org/10.1007/s11434-014-0498-9openalex-snapshot
Bacterial peptide deformylase inhibitor PMT analogs inhibit cancer cell growth by interacting with human peptide deformylase
inferred← citeshttps://doi.org/10.1007/s12010-015-1672-5openalex-snapshot
Virtual Screening and Molecular Dynamics Simulations from a Bank of Molecules of the Amazon Region Against Functional NS3-4A Protease-Helicase Enzyme of Hepatitis C Virus
inferred← citeshttps://doi.org/10.1007/s12551-013-0130-2openalex-snapshot
Receptor–ligand molecular docking
inferred← citeshttps://doi.org/10.1007/s12551-016-0247-1openalex-snapshot
Software for molecular docking: a review
inferred← citeshttps://doi.org/10.1007/s44337-025-00194-zopenalex-snapshot
Beyond analgesia: repurposing NSAIDs as a novel strategy in antivenom therapy against Naja nigricollis envenomation
inferred← citeshttps://doi.org/10.1016/b0-08-045044-x/00002-xopenalex-snapshot
Drug Discovery: Historical Perspective, Current Status, and Outlook
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/b0-08-045044-x/00273-xopenalex-snapshot
Nuclear Hormone Receptors: Insights for Drug Design from Structure and Modeling
inferred← citeshttps://doi.org/10.1016/b978-0-12-374194-3.00010-xopenalex-snapshot
In Silico Screening
inferred← citeshttps://doi.org/10.1016/b978-0-12-385950-1.00008-0openalex-snapshot
Targeting Serpins in High-Throughput and Structure-Based Drug Design
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/b978-0-12-409547-2.12352-2openalex-snapshot
Molecular Docking—A Solved Problem?
inferred← citeshttps://doi.org/10.1016/b978-0-12-417205-0.00004-3openalex-snapshot
Strategies in the Search for New Lead Compounds or Original Working Hypotheses
inferred← citeshttps://doi.org/10.1016/b978-0-12-417205-0.00006-7openalex-snapshot
In Silico Screening
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/b978-0-12-822312-3.00001-1openalex-snapshot
Best Practices for Docking-Based Virtual Screening
inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00025-4openalex-snapshot
Molecular Docking: A Contemporary Story About Food Safety
inferred← citeshttps://doi.org/10.1016/b978-0-323-85681-2.00005-7openalex-snapshot
Molecular docking and dynamics simulations of novel drug targets
inferred← citeshttps://doi.org/10.1016/b978-0-323-90608-1.00003-4openalex-snapshot
Structure-based drug design (SBDD)
inferred← citeshttps://doi.org/10.1016/b978-0-323-90608-1.00005-8openalex-snapshot
Fundamental considerations in drug design
inferred← citeshttps://doi.org/10.1016/b978-0-443-15457-7.00027-7openalex-snapshot
In silico techniques for screening of key secondary metabolites of medicinal plants
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/b978-0-443-44181-3.00002-3openalex-snapshot
Advances in cancer drug discovery integrated with computational approaches
inferred← citeshttps://doi.org/10.1016/b978-012744481-9/50009-xopenalex-snapshot
STRATEGIES IN THE SEARCH FOR NEW LEAD COMPOUNDS OR ORIGINAL WORKING HYPOTHESES
inferred← citeshttps://doi.org/10.1016/b978-012744481-9/50013-1openalex-snapshot
ELECTRONIC SCREENING: LEAD FINDING FROM DATABASE MINING
inferred← citeshttps://doi.org/10.1016/b978-044452220-7/50073-3openalex-snapshot
High throughput in-silico screening of large ligand databases for rational drug design
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.bbapap.2010.04.008openalex-snapshot
Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening
inferred← citeshttps://doi.org/10.1016/j.bbrc.2009.11.125openalex-snapshot
Rational design of aminoacyl-tRNA synthetase specific for p-acetyl-l-phenylalanine
inferred← citeshttps://doi.org/10.1016/j.bcp.2009.09.028openalex-snapshot
Chain termination and inhibition of mammalian poly(A) polymerase by modified ATP analogues
inferred← citeshttps://doi.org/10.1016/j.biopha.2021.112459openalex-snapshot
Discovery of a novel cyclin-dependent kinase 8 inhibitor with an oxindole core for anti-inflammatory treatment
inferred← citeshttps://doi.org/10.1016/j.biopha.2021.112580openalex-snapshot
Identification and analysis of a selective DYRK1A inhibitor
inferred← citeshttps://doi.org/10.1016/j.biopha.2022.113585openalex-snapshot
Structure-based virtual screening discovers novel kidney-type glutaminase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmc.2003.12.023openalex-snapshot
A structure-based strategy to identify new molecular scaffolds targeting the bacterial ribosomal A-site
inferred← citeshttps://doi.org/10.1016/j.bmc.2005.04.037openalex-snapshot
Docking simulation with a purine nucleoside specific homology model of deoxycytidine kinase, a target enzyme for anticancer and antiviral therapy
inferred← citeshttps://doi.org/10.1016/j.bmc.2007.11.076openalex-snapshot
Docking and hydropathic scoring of polysubstituted pyrrole compounds with antitubulin activity
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.02.054openalex-snapshot
Structure-based virtual screening of Src kinase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmc.2009.08.022openalex-snapshot
Computational modeling of novel inhibitors targeting the Akt pleckstrin homology domain
inferred← citeshttps://doi.org/10.1016/j.bmc.2015.01.016openalex-snapshot
Computer-aided discovery of aminopyridines as novel JAK2 inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2004.06.091openalex-snapshot
GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm
inferred← citeshttps://doi.org/10.1016/j.bmcl.2009.02.034openalex-snapshot
Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs)
inferred← citeshttps://doi.org/10.1016/j.bmcl.2011.09.127openalex-snapshot
Synthesis and docking study of 2-phenylaminopyrimidine Abl tyrosine kinase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2016.03.048openalex-snapshot
Discovery of KDM5A inhibitors: Homology modeling, virtual screening and structure–activity relationship analysis
inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.05.002openalex-snapshot
Discovery of pyrazolo[1,5-a]pyrimidine-3-carbonitrile derivatives as a new class of histone lysine demethylase 4D (KDM4D) inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2022.128909openalex-snapshot
Monoterpene substituted thiazolidin-4-ones as novel TDP1 inhibitors: Synthesis, biological evaluation and docking
inferred← citeshttps://doi.org/10.1016/j.chemosphere.2021.133422openalex-snapshot
Computational methods on food contact chemicals: Big data and in silico screening on nuclear receptors family
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2004.09.003openalex-snapshot
Development of KiBank, a database supporting structure-based drug design
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2024.108020openalex-snapshot
Computational prediction for designing novel ketonic derivatives as potential inhibitors for breast cancer: A trade-off between drug likeness and inhibition potency
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