Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas
| Autor: | Melis Kayikci, Charles N. J. Ravarani, Tilman Flock, James Scott-Brown, AJ Venkatakrishnan, M. Madan Babu |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Models
Molecular 0301 basic medicine Rhodopsin 030103 biophysics Computer science Non covalent Protein Data Bank (RCSB PDB) Computational biology Crystallography X-Ray Ligands Protein Structure Secondary Article 03 medical and health sciences Protein structure Structural Biology Protein Interaction Mapping Humans Databases Protein Molecular Biology Protein secondary structure Polymorphism Genetic Computational Biology Proteins Hydrogen Bonding DNA Visualization 030104 developmental biology Mutation Allosteric Site Biomarkers Protein Binding |
| Zdroj: | Nature structural & molecular biology |
| ISSN: | 1545-9985 1545-9993 |
| DOI: | 10.1038/s41594-017-0019-z |
| Popis: | Visualizations of biomolecular structures empower us to gain insights into biological functions, generate testable hypotheses, and communicate biological concepts. Typical visualizations (such as ball and stick) primarily depict covalent bonds. In contrast, non-covalent contacts between atoms, which govern normal physiology, pathogenesis, and drug action, are seldom visualized. We present the Protein Contacts Atlas, an interactive resource of non-covalent contacts from over 100,000 PDB crystal structures. We developed multiple representations for visualization and analysis of non-covalent contacts at different scales of organization: atoms, residues, secondary structure, subunits, and entire complexes. The Protein Contacts Atlas enables researchers from different disciplines to investigate diverse questions in the framework of non-covalent contacts, including the interpretation of allostery, disease mutations and polymorphisms, by exploring individual subunits, interfaces, and protein-ligand contacts and by mapping external information. The Protein Contacts Atlas is available at http://www.mrc-lmb.cam.ac.uk/pca/ and also through PDBe. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink