دورية أكاديمية
MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.
| العنوان: | MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions. |
|---|---|
| المؤلفون: | Rodriguez DCP; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, USA., Weber KC; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, USA., Sundberg B; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, USA., Glasgow A; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, USA. |
| المصدر: | Protein science : a publication of the Protein Society [Protein Sci] 2024 Aug; Vol. 33 (8), pp. e5027. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet ISSN: 1469-896X (Electronic) Linking ISSN: 09618368 NLM ISO Abbreviation: Protein Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2001- : Woodbury, NY : Cold Spring Harbor Laboratory Press Original Publication: New York, N.Y. : Cambridge University Press, c1992- |
| مواضيع طبية MeSH: | Software* , Proteins*/chemistry , Proteins*/metabolism, Ligands ; Protein Binding ; Models, Molecular |
| مستخلص: | Quantitative tools to compile and analyze biomolecular interactions among chemically diverse binding partners would improve therapeutic design and aid in studying molecular evolution. Here we present Mapping Areas of Genetic Parsimony In Epitopes (MAGPIE), a publicly available software package for simultaneously visualizing and analyzing thousands of interactions between a single protein or small molecule ligand (the "target") and all of its protein binding partners ("binders"). MAGPIE generates an interactive three-dimensional visualization from a set of protein complex structures that share the target ligand, as well as sequence logo-style amino acid frequency graphs that show all the amino acids from the set of protein binders that interact with user-defined target ligand positions or chemical groups. MAGPIE highlights all the salt bridge and hydrogen bond interactions made by the target in the visualization and as separate amino acid frequency graphs. Finally, MAGPIE collates the most common target-binder interactions as a list of "hotspots," which can be used to analyze trends or guide the de novo design of protein binders. As an example of the utility of the program, we used MAGPIE to probe how different antibody fragments bind a viral antigen; how a common metabolite binds diverse protein partners; and how two ligands bind orthologs of a well-conserved glycolytic enzyme for a detailed understanding of evolutionarily conserved interactions involved in its activation and inhibition. MAGPIE is implemented in Python 3 and freely available at https://github.com/glasgowlab/MAGPIE, along with sample datasets, usage examples, and helper scripts to prepare input structures. (© 2024 The Protein Society.) |
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| معلومات مُعتمدة: | R00GM135529 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: biomolecular interactions; computational drug design; protein‐small molecule binding; protein–ligand interactions; protein–protein interactions |
| المشرفين على المادة: | 0 (Ligands) 0 (Proteins) |
| تواريخ الأحداث: | Date Created: 20240711 Date Completed: 20240711 Latest Revision: 20240714 |
| رمز التحديث: | 20240714 |
| مُعرف محوري في PubMed: | PMC11237554 |
| DOI: | 10.1002/pro.5027 |
| PMID: | 38989559 |
| قاعدة البيانات: | MEDLINE |
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