Oct 25, 2008

Voronoia: analyzing packing in protein structures

Nucleic Acids Research
Kristian RotherRobert Preissner


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 acce...Continue Reading

  • References19
  • Citations45


Mentioned in this Paper

Acquired Ichthyosis
Ligand Binding
Body Cavities
Dental Caries
Protein Conformation
Virtual Systems
PHLPP1 wt Allele

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Synthetic Genetic Array Analysis

Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

Head And Neck Squamous Cell Carcinoma

Squamous cell carcinomas account for >90% of all tumors in the head and neck region. Head and neck squamous cell carcinoma incidence has increased dramatically recently with little improvement in patient outcomes. Here is the latest research on this aggressive malignancy.

Signaling in Adult Neurogenesis

Neural stem cells play a critical role in the production of neuronal cells in neurogenesis is of great importance. Of interest is the role signalling mechanisms in adult neurogenesis. Discover the latest research on signalling in adult neurogenesis.

Psychiatric Chronotherapy

Psychiatric Chronotherapy considers the circadian rhythm as a major factor for optimizing therapeutic efficacy of psychiatric interventions. Discover the latest research on Psychiatric Chronotherapy here.

Epigenetic Memory

Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.

Bone Marrow Neoplasms

Bone Marrow Neoplasms are cancers that occur in the bone marrow. Discover the latest research on Bone Marrow Neoplasms here.

Related Papers

Journal of Molecular Biology
S F AltschulD J Lipman
PLoS Computational Biology
Shrihari Sonavane, Pinak Chakrabarti
The Journal of Neuroscience : the Official Journal of the Society for Neuroscience
Victor A StreltsovStewart D Nuttall
Nucleic Acids Research
Liisa Holm, Päivi Rosenström
© 2020 Meta ULC. All rights reserved