ArticleJournal of chemical information and modeling2021
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- New paradigm of q-CAR drug development targeting disease-specific protein conformations.npj drug discovery · 2026Review
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- Integrated computational-experimental pipeline for CHK1 inhibitor discovery: structure-based identification of novel chemotypes with anticancer activity.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Weighted Ensemble Simulations Reveal Novel Conformations and Modulator Effects in Hepatitis B Virus Capsid Assembly.Journal of chemical theory and computation · 2025Article
- Modeling Boltzmann-weighted structural ensembles of proteins using artificial intelligence-based methods.Current opinion in structural biology · 2025Review
- In silico study to identify novel NEK7 inhibitors from natural sources by a combination strategy.Molecular diversity · 2025Article
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- In silico docking and molecular dynamics for the discovery of inhibitors of enteric methane production in ruminants - A review.Animal bioscience · 2025Article
- Potent and Selective Human 5-HTJournal of medicinal chemistry · 2024Article
- Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE.eLife · 2024Article
- An Overview of Crosslinked Enzyme Aggregates: Concept of Development and Trends of Applications.Applied biochemistry and biotechnology · 2024Review
- Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE.ArXiv · 2024Article
- Structure-Based Discovery of Mouse Trace Amine-Associated Receptor 5 Antagonists.Journal of chemical information and modeling · 2023Article
- Discovery of Chemical Scaffolds as Lysophosphatidic Acid Receptor 1 Antagonists: Virtual Screening,ACS omega · 2023Article
- CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.Journal of chemical information and modeling · 2023Article
- Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection.International journal of molecular sciences · 2023Article
- Article
- PDBspheres: a method for finding 3D similarities in local regions in proteins.NAR genomics and bioinformatics · 2022Article
- Heat Shock Protein 90 (HSP90) Inhibitors as Anticancer Medicines: A Review on the Computer-Aided Drug Discovery Approaches over the Past Five Years.Computational and mathematical methods in medicine · 2022Review
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4 authors.
Funding
Abstract
The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF
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