Automatic target selection for structural genomics on eukaryotes.

Target space for structural genomics revisited

MOTIVATION Structural genomics eventually aims at determining structures for all proteins. However, in the beginning experimentalists are likely to focus on globular proteins to achieve a rapid basic coverage of protein sequence space. How many proteins will structural genomics have to target? How many proteins will be excluded since we already have structural information for these or since the...

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches.

Structural genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the "Pfam5000" strategy, which involves selecting the 5000 ...

Target selection for structural genomics based on ProtoNet classification

Motivation: Structural genomics projects aim to solve a large number of protein structures to eventually represent the entire protein space. To this end it is necessary to increase the rate at which new families, superfamilies and folds are discovered. To facilitate that, strategies to improve the selection of targets for structural determination are needed. An important component in the design...

Prot - 00199 - 2004 - R 1 Implications of structural genomics target selection strategies : Pfam 5000 , whole genome , and random approaches

Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores.

Ketopatoate reductase (KPR) is the second enzyme in the pantothenate (vitamin B(5)) biosynthesis pathway, an essential metabolic pathway identified as a potential target for new antimicrobials. The sequence similarity among putative KPRs is limited and KPR itself belongs to a large superfamily of 6-phosphogluconate dehydrogenases. Therefore, it is necessary to discriminate between true and othe...