ArticlePLoS computational biology2019
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
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- Benchmarking co-folding methods to predict the structures of covalent protein-ligand complexes.Acta pharmacologica Sinica · 2026Article
- AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2.Nature methods · 2026Article
- Molecular Strategies of Carbohydrate Binding to Intrinsically Disordered Regions in Bacterial Transcription Factors.International journal of molecular sciences · 2026Article
- Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening.Journal of chemical information and modeling · 2026Article
- Flexible protein-ligand docking with diffusion-based side-chain packing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- LABind: identifying protein binding ligand-aware sites via learning interactions between ligand and protein.Nature communications · 2025Article
- Exploration of Multiconformers to Extract Information About Structural Deformation Undergone by a Protein Target: Illustration on the Bcl-xL Target.Molecules (Basel, Switzerland) · 2025Article
- Computational analysis of polymorphic residues in maltose and maltotriose transporters of a wildOpen life sciences · 2025Article
- In silico identification of novel ligands targeting stress-related human FKBP5 protein in mental disorders.PloS one · 2025Article
- AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.International journal of molecular sciences · 2024Article
- Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation.Journal of molecular evolution · 2024Article
- Structure optimization and molecular dynamics studies of new tumor-selectiveJournal of enzyme inhibition and medicinal chemistry · 2024Article
- The Art and Science of Molecular Docking.Annual review of biochemistry · 2024Review
- Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme.Scientific reports · 2024Article
- DiffBindFR: an SE(3) equivariant network for flexible protein-ligand docking.Chemical science · 2024Article
- Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP.Science advances · 2024Article
- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines.JACS Au · 2024Article
- Real-Time Determination of Intracellular cAMP Reveals Functional Coupling of GInternational journal of molecular sciences · 2024Article
- Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines.bioRxiv : the preprint server for biology · 2024Article
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4 authors.
Funding
Abstract
Understanding how ligand binding influences protein flexibility is important, especially in rational drug design. Protein flexibility upon ligand binding is analyzed herein using 305 proteins with 2369 crystal structures with ligands (holo) and 1679 without (apo). Each protein has at least two apo and two holo structures for analysis. The inherent variation in structures with and without ligands is first established as a baseline. This baseline is then compared to the change in conformation in going from the apo to holo states to probe induced flexibility. The inherent backbone flexibility across the apo structures is roughly the same as the variation across holo structures. The induced backbone flexibility across apo-holo pairs is larger than that of the apo or holo states, but the increase in RMSD is less than 0.5 Å. Analysis of χ1 angles revealed a distinctly different pattern with significant influences seen for ligand binding on side-chain conformations in the binding site. Within the apo and holo states themselves, the variation of the χ1 angles is the same. However, the data combining both apo and holo states show significant displacements. Upon ligand binding, χ1 angles are frequently pushed to new orientations outside the range seen in the apo states. Influences on binding-site variation could not be easily attributed to features such as ligand size or x-ray structure resolution. By combining these findings, we find that most binding site flexibility is compatible with the common practice in flexible docking, where backbones are kept rigid and side chains are allowed some degree of flexibility.
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