ArticleJournal of chemical theory and computation2016
Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking.
Article in Journal of chemical theory and computation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Molecular correlates of vaccine-induced protection against typhoid fever.The Journal of clinical investigation · 2023Trial
- Chemoenzymatic Synthesis of Well-Defined α(2,8)- and α(2,9)-Linked Oligosialosides.Angewandte Chemie (International ed. in English) · 2026Article
- The conserved Pss exopolysaccharide is a common component ofJournal of bacteriology · 2026Article
- Metabolism of β-mannans by representative, understudied Bacillota species from the human colon.FEMS microbiology ecology · 2026Article
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Validated FSP1 Inhibitors.bioRxiv : the preprint server for biology · 2026Article
- Glycophagy is an ancient bilaterian pathway supporting metabolic adaptation through STBD1 structural evolution.Communications biology · 2026Article
- In vitro and in silico studies of anticancer activities of pectic acid and pectin oligosaccharide in Epstein-Barr virus-positive nasopharyngeal carcinoma.Journal of computer-aided molecular design · 2025Article
- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
- Precision-Engineered Dermatan Sulfate-Mimetic Glycopolymers for Multi-Targeted SARS-CoV-2 Inhibition.Marine drugs · 2025Article
- Atom-level machine learning of protein-glycan interactions and cross-chiral recognition in glycobiology.Science advances · 2025Article
- Towards Understanding the Basis of Brucella Antigen-Antibody Specificity.Molecules (Basel, Switzerland) · 2025Article
- FeatureDock for protein-ligand docking guided by physicochemical feature-based local environment learning using transformer.npj drug discovery · 2025Article
- Dual functional POGases from bacteria encompassing broader O-glycanase and adhesin activities.Nature communications · 2025Article
- Sticky organisms create underwater biological adhesives driven by interactions between EGF- and GlcNAc- containing polysaccharides.Nature communications · 2025Article
- Identification and Analysis of Anticancer Therapeutic Targets from the Polysaccharide Krestin (PSK) and Polysaccharopeptide (PSP) Using Inverse Docking.Molecules (Basel, Switzerland) · 2024Article
- Modeling Protein-Glycan Interactions with HADDOCK.Journal of chemical information and modeling · 2024Article
- Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification.Nature communications · 2024Article
- Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.PLoS computational biology · 2024Article
- Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Molecular docking programs are primarily designed to align rigid, drug-like fragments into the binding sites of macromolecules and frequently display poor performance when applied to flexible carbohydrate molecules. A critical source of flexibility within an oligosaccharide is the glycosidic linkages. Recently, Carbohydrate Intrinsic (CHI) energy functions were reported that attempt to quantify the glycosidic torsion angle preferences. In the present work, the CHI-energy functions have been incorporated into the AutoDock Vina (ADV) scoring function, subsequently termed Vina-Carb (VC). Two user-adjustable parameters have been introduced, namely, a CHI- energy weight term (chi_coeff) that affects the magnitude of the CHI-energy penalty and a CHI-cutoff term (chi_cutoff) that negates CHI-energy penalties below a specified value. A data set consisting of 101 protein-carbohydrate complexes and 29 apoprotein structures was used in the development and testing of VC, including antibodies, lectins, and carbohydrate binding modules. Accounting for the intramolecular energies of the glycosidic linkages in the oligosaccharides during docking led VC to produce acceptable structures within the top five ranked poses in 74% of the systems tested, compared to a success rate of 55% for ADV. An enzyme system was employed in order to illustrate the potential application of VC to proteins that may distort glycosidic linkages of carbohydrate ligands upon binding. VC represents a significant step toward accurately predicting the structures of protein-carbohydrate complexes. Furthermore, the described approach is conceptually applicable to any class of ligands that populate well-defined conformational states.
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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.