Alpha shape and Delaunay triangulation in studies of protein-related interactions

@article{Zhou2014AlphaSA,
  title={Alpha shape and Delaunay triangulation in studies of protein-related interactions},
  author={Weiqiang Zhou and Hong Yan},
  journal={Briefings in bioinformatics},
  year={2014},
  volume={15 1},
  pages={
          54-64
        }
}
In recent years, more 3D protein structures have become available, which has made the analysis of large molecular structures much easier. There is a strong demand for geometric models for the study of protein-related interactions. Alpha shape and Delaunay triangulation are powerful tools to represent protein structures and have advantages in characterizing the surface curvature and atom contacts. This review presents state-of-the-art applications of alpha shape and Delaunay triangulation in the… 

Figures and Tables from this paper

A Novel Geometry-Based Approach to Infer Protein Interface Similarity
TLDR
PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner, and can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
Alpha Complexes in Protein Structure Prediction
TLDR
It is argued that kinetic a-complexes can be used to reduce the computational effort of determining the potential energy when ``moving" from one configuration to a neighboring one and suggested that the applicability of a- complexes and kinetic a -complexes in protein related problems deserves investigation.
Dissecting the roles of local packing density and longer-range effects in protein sequence evolution
TLDR
It is shown that the Voronoi cell volume, when calculated relative to the geometric center of amino-acid side chains, behaves nearly identically to the relative solvent accessibility, and both can explain, on average, approximately 34% of the site-specific variation in evolutionary rate in a data set of 209 enzymes.
Measuring the shapes of macromolecules – and why it matters
TLDR
This paper addresses the connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules, and shows that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity.
Dissecting the roles of local packing density and longer‐range effects in protein sequence evolution
TLDR
It is concluded that instead of contrasting solvent accessibility and local packing density, future research should emphasize on the relative importance of immediate contacts and longer‐range effects on evolutionary variation.
Machine Learned Model for Solid Form Volume Estimation Based on Packing-Accessible Surface and Molecular Topological Fragments.
We present a machine learned model for predicting the volume of a homomolecular crystal based on the single-molecule structure, implemented in the open-source Python package for Molecular Volume
Characterizing and Predicting Protein Hinges for Mechanistic Insight.
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms.
TLDR
A novel point clouds segmentation method, PointSite, is proposed, which performs protein LBS identification at the atom-level in a protein-centric manner and can outperform previous methods in atom Intersection over Union (atom-IoU) by a large margin.
...
...

References

SHOWING 1-10 OF 78 REFERENCES
Voronoi and Voronoi-related tessellations in studies of protein structure and interaction.
  • A. Poupon
  • Chemistry
    Current opinion in structural biology
  • 2004
Interface surfaces for protein-protein complexes
TLDR
A definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram is presented and a hierarchy that distinguishes core and peripheral regions is defined, shown to have correlation with hot-spots in protein-protein interactions.
Interface surfaces for protein-protein complexes
TLDR
A geometric approach is taken and an algorithm is presented to study the geometric and topological properties of an interface surface formed by two or more proteins, thus paving the way for future biochemical studies of protein-protein interactions.
Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition?
TLDR
This analysis highlights differences in spatial relationships in different complexes and at different positions in a complex, which helps explain why there is no simple, general code for protein-DNA recognition.
Defining and characterizing protein surface using alpha shapes
The alpha shape of a molecule is a geometrical representation that provides a unique surface decomposition and a means to filter atomic contacts. We used it to revisit and unify the definition and
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
TLDR
A precise algorithm based on alpha shapes for measuring space‐filling‐based molecular models (such as van der Waals, solvent accessible, and molecular surface descriptions) is applied for accurate computation of the surface area and volume of cavities in several proteins.
Prediction of protein-protein interaction sites using patch analysis.
TLDR
A method for defining and analysing a series of residue patches on the surface of protein structures is used to predict the location of protein-protein interaction sites and is successful for 66% of the structures.
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
TLDR
The TOPOFIT method helps to detect conformational changes, topological differences in variable parts, which are particularly important for studies of variations in active/ binding sites and protein classification.
Modelling protein docking using shape complementarity, electrostatics and biochemical information.
TLDR
A protein docking study was performed for two classes of biomolecular complexes: six enzyme/inhibitor and four antibody/antigen and tested the native rather than the complexed forms of the proteins to address the more scientifically interesting problem of predictive docking.
...
...