Mapping the Protein Universe

@article{Holm1996MappingTP,
  title={Mapping the Protein Universe},
  author={Liisa Holm and Chris Sander},
  journal={Science},
  year={1996},
  volume={273},
  pages={595 - 602}
}
The comparison of the three-dimensional shapes of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations, reaching back billions of years, between protein molecules. Protein shape comparison also improves tools for identifying gene functions in genome databases by… 
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1,502 Citations
Highly Influential Citations
111
Background Citations
319
Methods Citations
289
Results Citations
7

1,502 Citations

A global representation of the protein fold space
TLDR
A 3D map of the protein fold space in which structurally related folds are represented by spatially adjacent points reveals a high-level organization of the fold space that is intuitively interpretable.
Bridging protein local structures and protein functions
TLDR
The repertoire of methods currently being applied in the field of in silico annotation of protein function based on the accumulation of vast amounts of sequence and structure data is summarized and newly developed structure-based methods are emphasized, which are able to identify locally structural motifs and reveal their relationship with protein functions.
Geometric and topological methods in protein structure analysis
TLDR
This thesis describes efficient computational methods for describing and comparing molecular structures by combining both geometric and topological approaches and describes an efficient algorithm to find promising initial relative placements of the proteins.
Expanding protein universe and its origin from the biological Big Bang
TLDR
This work has discovered that the universe of protein structures is organized hierarchically into a scale-free network and attempts to glance at the very origin of life.
Comparing and modeling protein structure
TLDR
The first part of this work focuses on protein structural alignment, namely, the comparison of two structures and formalizes this problem as the optimization of a geometric similarity score over the space of rigid body transformations, leading to an approximate polynomial time alignment algorithm.
Representation of the Protein Universe using Classifications, Maps, and Networks
TLDR
Different protein qualities were revealed in each study; many point out the uniqueness of domains of the alpha/beta SCOP (structural classification of proteins) class.
The structure of the protein universe and genome evolution
TLDR
These findings suggest that genome evolution is driven by extremely general mechanisms based on the preferential attachment principle, and that protein folds and families encoded in diverse genomes show similar size distributions with notable mathematical properties.
Analysis and algorithms for protein sequence–structure alignment
Protein folds: molecular systematics in three dimensions
TLDR
All basic protein folds will likely be determined in the near future, laying the foundation for a comprehensive understanding of the biochemical and cellular functions of whole organisms.
Overview of structural genomics: from structure to function.
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References

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TLDR
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