ArticleJournal of molecular graphics & modelling2009
Visualisation of cyclic and multi-branched molecules with VMD.
Article in Journal of molecular graphics & modelling, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- Intrinsic and environmental modulation of stereoselective aldol organocatalyzed reactions by proline-containing lipopeptides.RSC advances · 2024Article
- Conformational comparisons of Pasteurella multocida types B and E and structurally related capsular polysaccharides.Glycobiology · 2023Article
- Clustering molecular dynamics conformations of the CC'-loop of the PD-1 immuno-checkpoint receptor.Computational and structural biotechnology journal · 2023Article
- Comparative Molecular Modelling of Capsular Polysaccharide Conformations inFrontiers in molecular biosciences · 2022Article
- Molecular dynamics identifies semi-rigid domains in the PD-1 checkpoint receptor bound to its natural ligand PD-L1.Frontiers in bioengineering and biotechnology · 2022Article
- Modeling of pneumococcal serogroup 10 capsular polysaccharide molecular conformations provides insight into epitopes and observed cross-reactivity.Frontiers in molecular biosciences · 2022Article
- Cross-reactivity of Haemophilus influenzae type a and b polysaccharides: molecular modeling and conjugate immunogenicity studies.Glycoconjugate journal · 2021Article
- Conformational and Immunogenicity Studies of theVaccines · 2021Article
- Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase.Structure (London, England : 1993) · 2021Article
- Review
- Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations.The journal of physical chemistry. B · 2020Article
- COVID-19 Infection Detection and Prevention by SARS-CoV-2 Active Antigens: A Synthetic Vaccine Approach.Vaccines · 2020Article
- Molecular Modeling of theVaccines · 2020Article
- Three-Dimensional Structures of Carbohydrates and Where to Find Them.International journal of molecular sciences · 2020Review
- Article
- Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen-antibody binding.Beilstein journal of organic chemistry · 2020Article
- Computational tools for drawing, building and displaying carbohydrates: a visual guide.Beilstein journal of organic chemistry · 2020Review
- Conformation and Cross-Protection in Group B Streptococcus Serotype III andPharmaceuticals (Basel, Switzerland) · 2019Article
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4 authors.
Funding
Abstract
We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone package for carbohydrates. PaperChain highlights each ring in a molecular structure with a polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds with a ribbon that twists according to the relative orientation of successive sugar residues. Combination of these novel algorithms and new ring selection statements with the large set of visualisations already available in VMD allows for unprecedented flexibility in the level of detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein structures, as well as other cyclic structures. We highlight the efficacy of these algorithms with selected illustrative examples, clearly demonstrating the value of the new visualisations, not only for structure validation, but also for facilitating insights into molecular structure and mechanism.
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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.