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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1,503 Citations
Highly Influential Citations
111
Background Citations
320
Methods Citations
289
Results Citations
7

1,503 Citations

Geometric and topological methods in protein structure analysis
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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.
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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
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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
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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, functions and evolution.
TLDR
The evolution of proteins and their functions is reviewed from a structural perspective in the light of the current database, finding that the number of new topologies is still increasing, although 25 new structures are now determined for each new topology.
Local Structure Comparison of Proteins
Algorithms exploiting the chain structure of proteins
TLDR
Three algorithms addressing fundamental problems in computational structural biology are presented, including an automatic method for completing partial models of protein structures resolved using X-ray crystallography, and a method for speeding up Monte Carlo simulation of proteins.
Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.
  • R. SánchezA. Sali
  • Biology, Engineering
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
The fold assignment, comparative protein structure modeling, and model evaluation were automated completely and resulted in all-atom 3D models for substantial segments of 1,071 of the yeast proteins, only 40 of which have had their 3D structure determined experimentally.
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