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Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening

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Outgoing claims: the papers this work cites, builds on, or argues with.

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A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape
inferredcites →https://doi.org/10.1002/9783527633326openalex-snapshot
Virtual Screening
inferredcites →https://doi.org/10.1002/qsar.200290002openalex-snapshot
Identification of Diverse Database Subsets using Property‐Based and Fragment‐Based Molecular Descriptions
inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
inferredcites →https://doi.org/10.1021/ci100031xopenalex-snapshot
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci100062nopenalex-snapshot
Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments
inferredcites →https://doi.org/10.1021/ci100161zopenalex-snapshot
Protein Kinases: Docking and Homology Modeling Reliability
inferredcites →https://doi.org/10.1021/ci300314kopenalex-snapshot
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures
inferredcites →https://doi.org/10.1021/ci300463gopenalex-snapshot
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking
inferredcites →https://doi.org/10.1021/ci400572xopenalex-snapshot
Data Set Modelability by QSAR
inferredcites →https://doi.org/10.1021/ci600426eopenalex-snapshot
Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem
inferredcites →https://doi.org/10.1021/ci700052xopenalex-snapshot
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
inferredcites →https://doi.org/10.1021/ci700253hopenalex-snapshot
Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy
inferredcites →https://doi.org/10.1021/ci7004274openalex-snapshot
Cross-Docking of Inhibitors into CDK2 Structures. 1
inferredcites →https://doi.org/10.1021/ci700428dopenalex-snapshot
Cross-Docking of Inhibitors into CDK2 Structures. 2
inferredcites →https://doi.org/10.1021/ci8002254openalex-snapshot
Protein−Ligand Docking against Non-Native Protein Conformers
inferredcites →https://doi.org/10.1021/jm030209yopenalex-snapshot
Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm401411zopenalex-snapshot
Molecular Similarity in Medicinal Chemistry
inferredcites →https://doi.org/10.1038/msb.2011.5openalex-snapshot
Analysis of multiple compound–protein interactions reveals novel bioactive molecules
inferredcites →https://doi.org/10.1038/nrd941openalex-snapshot
Integration of virtual and high-throughput screening
inferredcites →https://doi.org/10.1073/pnas.1119817109openalex-snapshot
Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase
inferredcites →https://doi.org/10.1371/journal.pone.0057888openalex-snapshot
Profile of the GSK Published Protein Kinase Inhibitor Set Across ATP-Dependent and-Independent Luciferases: Implications for Reporter-Gene Assays
inferredcites →https://doi.org/10.2174/138620709789824682openalex-snapshot
Structure-Based Virtual Ligand Screening: Recent Success Stories
inferredcites →https://doi.org/10.2174/138955708785132792openalex-snapshot
Synergies of Virtual Screening Approaches

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Docking, Scoring, and Virtual Screening in Drug Discovery
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In Silico Studies Designed to Select Sesquiterpene Lactones with Potential Antichagasic Activity from an In‐House Asteraceae Database
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2‐Phenyloxazole‐4‐carboxamide as a Scaffold for Selective Inhibition of Human Monoamine Oxidase B
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Carbonic Anhydrase Inhibitors: Identifying Therapeutic Cancer Agents Through Virtual Screening
inferred← citeshttps://doi.org/10.1007/s10822-015-9856-1openalex-snapshot
Ligand- and receptor-based docking with LiBELa
inferred← citeshttps://doi.org/10.1007/s10822-023-00544-yopenalex-snapshot
Open-ComBind: harnessing unlabeled data for improved binding pose prediction
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Understanding structural characteristics of PARP-1 inhibitors through combined 3D-QSAR and molecular docking studies and discovery of new inhibitors by multistage virtual screening
inferred← citeshttps://doi.org/10.1007/s12033-024-01200-yopenalex-snapshot
Structure and Ligand Based Virtual Screening and MPO Topological Analysis of Triazolo Thiadiazepine-fused Coumarin Derivatives as Anti-Parkinson Drug Candidates
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Hit and Lead Generation Strategies
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12330-3openalex-snapshot
Label-Free Screening Technologies
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Modern Tools and Techniques in Computer-Aided Drug Design
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Big Data in Drug Discovery
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Selection of protein conformations for structure-based polypharmacology studies
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Challenging clinically unresponsive medullary thyroid cancer: Discovery and pharmacological activity of novel RET inhibitors
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Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors
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In-silico studies for the development of novel RET inhibitors for cancer treatment
inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.08.005openalex-snapshot
Molecular fingerprint similarity search in virtual screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01087openalex-snapshot
Screening for Inhibitors of Main Protease in SARS-CoV-2: In Silico and In Vitro Approach Avoiding Peptidyl Secondary Amides
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00644openalex-snapshot
Virtual Screening in the Cloud Identifies Potent and Selective ROS1 Kinase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00745openalex-snapshot
Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00331openalex-snapshot
Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02855openalex-snapshot
Combined Modeling Approaches for Assessing Sodium-Iodide Symporter Inhibition
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00174openalex-snapshot
SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00290openalex-snapshot
Computational Modeling of β-Secretase 1 (BACE-1) Inhibitors Using Ligand Based Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00821openalex-snapshot
Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c02227openalex-snapshot
Decision Making in Structure-Based Drug Discovery: Visual Inspection of Docking Results
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c01199openalex-snapshot
Discovery of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 Main Protease through Computer-Aided Drug Design
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Computational Chemistry on a Budget: Supporting Drug Discovery with Limited Resources
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Compound Ranking Based on Fuzzy Three-Dimensional Similarity Improves the Performance of Docking into Homology Models of G-Protein-Coupled Receptors
inferred← citeshttps://doi.org/10.1021/ci5003735openalex-snapshot
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA
inferred← citeshttps://doi.org/10.1038/s41598-018-36179-5openalex-snapshot
ImmtorLig_DB: repertoire of virtually screened small molecules against immune receptors to bolster host immunity
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Data-driven assessment of bioisosteric replacements and their influence on off-target activity profiles
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Identification of potential Aurora kinase-C protein inhibitors: an amalgamation of energy minimization, virtual screening, prime MMGBSA and AutoDock
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Pharmacore maping based on docking, ADME/toxicity, virtual screening on 3,5-dimethyl-1,3,4-hexanetriol and dodecanoic acid derivates for anticancer inhibitors
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Prospective Assessment of Virtual Screening Heuristics Derived Using a Novel Fusion Score
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EC-Conf: A ultra-fast diffusion model for molecular conformation generation with equivariant consistency
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Synthesis and Molecular Docking Studies of Triazole Conjugated Novel 2,4-Disubstituted Thiazole Derivatives as CDK2 Inhibitors
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Screening for inhibitors of main protease in SARS-CoV-2: in silico and in vitro approach avoiding secondary amides
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Drug Repurposing and Polypharmacology to Fight SARS-CoV-2 Through Inhibition of the Main Protease
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Molecular Docking: Shifting Paradigms in Drug Discovery
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In Silico Repositioning of Cannabigerol as a Novel Inhibitor of the Enoyl Acyl Carrier Protein (ACP) Reductase (InhA)
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