Abstract
The use of graph-theoretical algorithms in the similarity searching of databases of 3-dimensional structures of macromolecules is discussed. The emphasis is on the structures of protein molecules, for which the vast majority of 3-dimensional information is available. An initial survey is made of the types of information available on macromolecular structure, and of the methods conventionally used to compare them. Next the use of graph theoretical algorithms to identify previously unrecognized similarities between the overall folds of proteins is described, using the structure of the HIV reverse transcriptase enzyme as an example. The further application of these methods to the problem of searching for three-dimensional patterns of sidechain functional groups is then considered, using the active site of influenza sialidase as an example.
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Abbreviations
- 3-D:
-
three-dimensional
- AIDS:
-
acquired immune deficiency syndrome
- ASCII:
-
American Standard Code for Information Interchange
- ATP:
-
adenosine triphosphate
- CPU:
-
central processor unit
- CSD:
-
Cambridge Structural Database
- DNA:
-
2′-deoxy-ribonucleic acid
- HIV:
-
Human Immunodeficiency Virus
- ICDH:
-
isocitrate dehydrogenase
- NMR:
-
nuclear magnetic resonance spectroscopy
- PDB:
-
Protein Data Bank
- RDBMS:
-
relational database management system
- RNA:
-
ribonucleic acid
- RNAase:
-
ribonuclease
- RT:
-
reverse transcriptase
- SSE:
-
secondary structure element
- UMP:
-
uracil monophosphate
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Artymiuk, P.J., Poirrette, A.R., Rice, D.W., Willett, P. (1995). The use of graph theoretical methods for the comparison of the structures of biological macromolecules. In: Sen, K.D. (eds) Molecular Similarity II. Topics in Current Chemistry, vol 174. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-58672-5_24
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