ArticleJournal of chemical information and modeling2014
Docking server for the identification of heparin binding sites on proteins.
Article in Journal of chemical information and modeling, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 78 citations in OpenAlex.
- CCHFV GP38 and GP85 interact with cell-surface glycosaminoglycans.Npj viruses · 2026Article
- Dynamic translocation of Inside-Out proteins to the cell surface underlies cellular adaptation to cancer-induced stress.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atom-level machine learning of protein-glycan interactions and cross-chiral recognition in glycobiology.Science advances · 2025Article
- Heparanase 2 Modulates Vascular Permeability via Heparan Sulfate-Dependent Growth Factor Signaling.Arteriosclerosis, thrombosis, and vascular biology · 2025Article
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- Amyloid-forming property of the N-terminal 1-70 residues of human apolipoprotein A-IV.Scientific reports · 2025Article
- Lymph-Node Inspired Hydrogels Enhance CAR Expression and Proliferation of CAR T Cells.ACS applied materials & interfaces · 2025Article
- A Robust Proteomics-Based Method for Identifying Preferred Protein Targets of Synthetic Glycosaminoglycan Mimetics.bioRxiv : the preprint server for biology · 2025Article
- Modeling Protein-Glycan Interactions with HADDOCK.Journal of chemical information and modeling · 2024Article
- Identification of heparin-binding amino acid residues in antibody HS4C3 with the potential to design antibodies against heparan sulfate domains.Glycobiology · 2024Article
- Article
- Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.Biomolecules · 2023Article
- Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein.Molecules (Basel, Switzerland) · 2023Article
- Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.Journal of chemical information and modeling · 2023Article
- The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells.Nature communications · 2023Article
- Heparin-Induced Changes of Vascular Endothelial Growth Factor (VEGFBiomolecules · 2023Article
- Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process.Molecules (Basel, Switzerland) · 2022Review
- Computer-Aided Multi-Epitope Vaccine Design againstInternational journal of environmental research and public health · 2022Article
- Heparin activation of protein Z-dependent protease inhibitor (ZPI) allosterically blocks protein Z activation through an extended heparin-binding site.The Journal of biological chemistry · 2022Article
- In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface.Process biochemistry (Barking, London, England) · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined pockets, rather than for docking polysaccharides to highly charged shallow crevices that usually bind heparin. We have extended the program PIPER and the automated protein-protein docking server ClusPro to heparin docking. Using a molecular mechanics energy function for scoring and the fast Fourier transform correlation approach, the method generates and evaluates close to a billion poses of a heparin tetrasaccharide probe. The docked structures are clustered using pairwise root-mean-square deviations as the distance measure. It was shown that clustering of heparin molecules close to each other but having different orientations and selecting the clusters with the highest protein-ligand contacts reliably predicts the heparin binding site. In addition, the centers of the five most populated clusters include structures close to the native orientation of the heparin. These structures can provide starting points for further refinement by methods that account for flexibility such as molecular dynamics. The heparin docking method is available as an advanced option of the ClusPro server at http://cluspro.bu.edu/ .
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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.