ArticleNucleic acids research2009
Voronoia: analyzing packing in protein structures.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography.IUCrJ · 2022Article
- Protposer: The web server that readily proposes protein stabilizing mutations with high PPV.Computational and structural biotechnology journal · 2022Article
- Voronoia 4-ever.Nucleic acids research · 2021Article
- 'International journal of molecular sciences · 2021Article
- Effect of mutation at oxyanion hole residu (H110F) on activity of Lk4 lipase.Biotechnology reports (Amsterdam, Netherlands) · 2021Article
- Crystallographic Structures of IlvN·Val/Ile Complexes: Conformational Selectivity for Feedback Inhibition of Aceto Hydroxy Acid Synthases.Biochemistry · 2019Article
- Networks of electrostatic and hydrophobic interactions modulate the complex folding free energy surface of a designed βα protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Characteristics of a PHD Finger Subtype.Biochemistry · 2018Article
- Article
- Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity.Scientific reports · 2016Article
- Structural Mechanism of the Interaction of Alzheimer Disease Aβ Fibrils with the Non-steroidal Anti-inflammatory Drug (NSAID) Sulindac Sulfide.The Journal of biological chemistry · 2015Article
- ProteinVolume: calculating molecular van der Waals and void volumes in proteins.BMC bioinformatics · 2015Article
- Solution structure and dynamics of human S100A14.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.Nucleic acids research · 2013Article
- Structural differences between thermophilic and mesophilic membrane proteins.Protein science : a publication of the Protein Society · 2012Article
- An amino acid packing code for α-helical structure and protein design.Journal of molecular biology · 2012Article
- Cloning, Baeyer-Villiger biooxidations, and structures of the camphor pathway 2-oxo-Δ(3)-4,5,5-trimethylcyclopentenylacetyl-coenzyme A monooxygenase of Pseudomonas putida ATCC 17453.Applied and environmental microbiology · 2012Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The packing of protein atoms is an indicator for their stability and functionality, and applied in determining thermostability, in protein design, ligand binding and to identify flexible regions in proteins. Here, we present Voronoia, a database of atomic-scale packing data for protein 3D structures. It is based on an improved Voronoi Cell algorithm using hyperboloid interfaces to construct atomic volumes, and to resolve solvent-accessible and -inaccessible regions of atoms. The database contains atomic volumes, local packing densities and interior cavities calculated for 61 318 biological units from the PDB. A report for each structure summarizes the packing by residue and atom types, and lists the environment of interior cavities. The packing data are compared to a nonredundant set of structures from SCOP superfamilies. Both packing densities and cavities can be visualized in the 3D structures by the Jmol plugin. Additionally, PDB files can be submitted to the Voronoia server for calculation. This service performs calculations for most full-atomic protein structures within a few minutes. For batch jobs, a standalone version of the program with an optional PyMOL plugin is available for download. The database can be freely accessed at: http://bioinformatics.charite.de/voronoia.
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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.