ReviewCurrent opinion in structural biology2008
Flexible ligand docking to multiple receptor conformations: a practical alternative.
Review in Current opinion in structural biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 179 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
179 citing papers in PubMed.
- In Silico Isomerization Produces Apt Negative Data for VHTS Validation.Journal of chemical information and modeling · 2026Article
- V-SYNTHES2-the next generation tool for structure-based virtual screening of giga-scale chemical spaces.npj drug discovery · 2026Article
- Dynamic stability-driven machine learning improves binding pose identification on human serum albumin.Journal of computer-aided molecular design · 2026Article
- Multi-target computational pipeline for discovery of pan-influenza neuraminidase inhibitors.Frontiers in pharmacology · 2026Article
- Rotation Conformational Effects of Selected Cytotoxic Cardiac Glycosides on Their Interactions with NaMolecules (Basel, Switzerland) · 2025Article
- V-synthes2 - the Next Generation Tool for Structure-based Virtual Screening of Giga-scale Chemical Spaces.Research square · 2025Article
- Symmetrical di-substituted phenylamino-RSC advances · 2025Article
- AI meets physics in computational structure-based drug discovery for GPCRs.npj drug discovery · 2025Review
- Computational prediction of CNP0387675 as a non-nucleoside inhibitor of MraY, from natural product-based multi-template screening againstFrontiers in microbiology · 2025Article
- Importance of Computer-aided Drug Design in Modern Pharmaceutical Research.Current drug discovery technologies · 2025Review
- Reliability of AlphaFold2 Models in Virtual Drug Screening: A Focus on Selected Class A GPCRs.International journal of molecular sciences · 2024Article
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Novel Scaffold Agonists of the αMolecules (Basel, Switzerland) · 2024Article
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Approaches to Backbone Flexibility in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Worth the Weight: Sub-Pocket EXplorer (SubPEx), a Weighted Ensemble Method to Enhance Binding-Pocket Conformational Sampling.Journal of chemical theory and computation · 2023Article
- Article
- Computational Exploration of Potential CFTR Binding Sites for Type I Corrector Drugs.Biochemistry · 2023Article
- A New Tool to Study the Binding Behavior of Intrinsically Disordered Proteins.International journal of molecular sciences · 2023Article
- Worth the weight: Sub-Pocket EXplorer (SubPEx), a weighted-ensemble method to enhance binding-pocket conformational sampling.bioRxiv : the preprint server for biology · 2023Article
119 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
State of the art docking algorithms predict an incorrect binding pose for about 50-70% of all ligands when only a single fixed receptor conformation is considered. In many more cases, lack of receptor flexibility results in meaningless ligand binding scores, even when the correct pose is obtained. Incorporating conformational rearrangements of the receptor binding pocket into predictions of both ligand binding pose and binding score is crucial for improving structure-based drug design and virtual ligand screening methodologies. However, direct modeling of protein binding site flexibility remains challenging because of the large conformational space that must be sampled, and difficulties remain in constructing a suitably accurate energy function. Here we show that using multiple fixed receptor conformations, either experimentally determined by crystallography or NMR, or computationally generated, is a practical shortcut that may improve docking calculations. In several cases, such an approach has led to experimentally validated predictions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.