ArticleJournal of computational chemistry2014
Importance of ligand conformational energies in carbohydrate docking: Sorting the wheat from the chaff.
Article in Journal of computational chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Generating 3D models of complex carbohydrates with GLYCAM-Web.Nature methods · 2026Article
- Crystal structure ofProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
- Activity-Based Tracking of Glycan Turnover in Microbiomes.Journal of the American Chemical Society · 2025Article
- Towards Understanding the Basis of Brucella Antigen-Antibody Specificity.Molecules (Basel, Switzerland) · 2025Article
- Identification and Analysis of Anticancer Therapeutic Targets from the Polysaccharide Krestin (PSK) and Polysaccharopeptide (PSP) Using Inverse Docking.Molecules (Basel, Switzerland) · 2024Article
- Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.PLoS computational biology · 2024Article
- Synthetic Glycans Reveal Determinants of Antibody Functional Efficacy against a Fungal Pathogen.ACS infectious diseases · 2024Article
- Computational toolbox for the analysis of protein-glycan interactions.Beilstein journal of organic chemistry · 2024Review
- Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.Biomolecules · 2023Article
- A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.iScience · 2023Article
- Molecular docking analysis of a dermatan sulfate tetra-saccharide to human alpha-L-iduronidase.Bioinformation · 2023Article
- Computationally guided conversion of the specificity of E-selectin to mimic that of Siglec-8.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans.Biomolecules · 2021Article
- Development and Evaluation of GlycanDock: A Protein-Glycoligand Docking Refinement Algorithm in Rosetta.The journal of physical chemistry. B · 2021Article
- A glycan FRET assay for detection and characterization of catalytic antibodies to theProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Carbohydrate-Protein Interactions: Advances and Challenges.Communications in information and systems · 2021Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.Cell host & microbe · 2020Article
- Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.Scientific reports · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Docking algorithms that aim to be applicable to a broad range of ligands suffer reduced accuracy because they are unable to incorporate ligand-specific conformational energies. Here, we develop a set of Carbohydrate Intrinsic (CHI) energy functions that quantify the conformational properties of oligosaccharides, based on the values of their glycosidic torsion angles. The relative energies predicted by the CHI energy functions mirror the conformational distributions of glycosidic linkages determined from a survey of oligosaccharide-protein complexes in the protein data bank. Addition of CHI energies to the standard docking scores in Autodock 3, 4.2, and Vina consistently improves pose ranking of oligosaccharides docked to a set of anticarbohydrate antibodies. The CHI energy functions are also independent of docking algorithm, and with minor modifications, may be incorporated into both theoretical modeling methods, and experimental NMR or X-ray structure refinement programs.
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Registered trials
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