ArticleChemMedChem2023
Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods.
Article in ChemMedChem, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Identification of potential MMP-8 inhibitors through virtual screening of natural product databases.In silico pharmacology · 2025Article
- Automated Adaptive Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2024Article
- Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations.Journal of chemical theory and computation · 2024Article
- Toward physics-based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants.Protein science : a publication of the Protein Society · 2024Review
- Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides.Frontiers in molecular biosciences · 2024Article
- Discovery of Potential Noncovalent Inhibitors of Dehydroquinate Dehydratase from Methicillin-ResistantPharmaceuticals (Basel, Switzerland) · 2023Article
- In Silico Discovery of Potential Inhibitors Targeting the RNA Binding Loop of ADAR2 and 5-HT2CR from Traditional Chinese Natural Compounds.International journal of molecular sciences · 2023Article
- Imidazole-4-N-acetamide Derivatives as a Novel Scaffold for Selective Targeting of Cyclin Dependent Kinases.Cancers · 2023Article
- Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2023Article
- Virtual Screening of a Marine Natural Product Database for In Silico Identification of a Potential Acetylcholinesterase Inhibitor.Life (Basel, Switzerland) · 2023Article
- Novel Anti-Acetylcholinesterase Effect ofLife (Basel, Switzerland) · 2023Article
- Novel Allosteric Effectors Targeting Human Transcription Factor TEAD.International journal of molecular sciences · 2023Article
- Molecular Structural Analysis of Porcine CMAH-Native Ligand Complex and High Throughput Virtual Screening to Identify Novel Inhibitors.Pathogens (Basel, Switzerland) · 2023Article
- Computational Exploration of Licorice for Lead Compounds againstMolecules (Basel, Switzerland) · 2023Article
- Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors.International journal of molecular sciences · 2023Article
- Computer-Aided Drug Design and Synthesis of Rhenium Clotrimazole Antimicrobial Agents.Antibiotics (Basel, Switzerland) · 2023Article
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9 authors.
Funding
Abstract
Prioritizing molecules for synthesis is a key role of computational methods within medicinal chemistry. Multiple tools exist for ranking molecules, from the cheap and popular molecular docking methods to more computationally expensive molecular-dynamics (MD)-based methods. It is often questioned whether the accuracy of the more rigorous methods justifies the higher computational cost and associated calculation time. Here, we compared the performance on ranking the binding of small molecules for seven scoring functions from five docking programs, one end-point method (MM/GBSA), and two MD-based free energy methods (PMX, FEP+). We investigated 16 pharmaceutically relevant targets with a total of 423 known binders. The performance of docking methods for ligand ranking was strongly system dependent. We observed that MD-based methods predominantly outperformed docking algorithms and MM/GBSA calculations. Based on our results, we recommend the application of MD-based free energy methods for prioritization of molecules for synthesis in lead optimization, whenever feasible.
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