BLASTing away preconceptions in crystallization trials
| Autor: | Janet Newman, Gabriel Abrahams |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Computer science
Biophysics 010402 general chemistry Crystallography X-Ray 01 natural sciences Biochemistry law.invention Research Communications 03 medical and health sciences Similarity (network science) Structural Biology law Genetics Amino Acid Sequence Crystallization Databases Protein 030304 developmental biology Sequence (medicine) 0303 health sciences Initial screen A protein Proteins computer.file_format Condensed Matter Physics Protein Data Bank 0104 chemical sciences Biological system computer Rock blasting |
| Zdroj: | Acta Crystallogr F Struct Biol Commun |
| ISSN: | 2053-230X |
| Popis: | Crystallization is in many cases a critical step for solving the three-dimensional structure of a protein molecule. Determining which set of chemicals to use in the initial screen is typically agnostic of the protein under investigation; however, crystallization efficiency could potentially be improved if this were not the case. Previous work has assumed that sequence similarity may provide useful information about appropriate crystallization cocktails; however, the authors are not aware of any quantitative verification of this assumption. This research investigates whether, given current information, one can detect any correlation between sequence similarity and crystallization cocktails. BLAST was used to quantitate the similarity between protein sequences in the Protein Data Bank, and this was compared with three estimations of the chemical similarities of the respective crystallization cocktails. No correlation was detected between proteins of similar (but not identical) sequence and their crystallization cocktails, suggesting that methods of determining screens based on this assumption are unlikely to result in screens that are better than those currently in use. |
| Databáze: | OpenAIRE |
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