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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
D²P²: database of disordered protein predictions
Matt E Oates1, Pedro Romero, Takashi Ishida
1Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK. Matt.Oates@bristol.ac.uk
Nucleic Acids Research
|December 4, 2012
Summary
The Database of Disordered Protein Prediction (D(2)P(2)) offers a comprehensive resource for analyzing protein disorder across many proteomes. It integrates multiple disorder prediction tools and structural domain data to explore disorder
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions but are challenging to characterize using traditional structural methods.
- Understanding the genomic distribution and evolutionary patterns of protein disorder is essential for comprehending protein function and evolution.
Purpose of the Study:
- To present the Database of Disordered Protein Prediction (D(2)P(2)), a centralized resource for analyzing protein disorder across diverse proteomes.
- To facilitate large-scale comparisons of various protein disorder prediction methods and their overlap with known protein structures.
Main Methods:
- A comprehensive set of protein disorder predictors (VL-XT, VSL2b, PrDOS, PV2, Espritz, IUPred) were applied to all protein sequences from 1765 complete proteomes.
- Predicted SCOP (Structural Classification of Proteins) domains from the SUPERFAMILY predictor were integrated with disorder predictions.
- Data were made available in downloadable formats (flat files, SQL tables) and through an interactive website with graphical annotations.
Main Results:
- The D(2)P(2) database provides integrated disorder and structure annotations for a vast number of proteins.
- It enables large-scale comparative analysis of disorder prediction algorithms and their relationship with protein structural domains.
- The database facilitates exploration of the genomic distribution and evolutionary context of protein disorder.
Conclusions:
- D(2)P(2) serves as a valuable resource for advancing the understanding of the interplay between protein disorder and structure.
- The integrated data aids in studying the genomic distribution and evolutionary history of disordered proteins.
- The interactive platform supports comparative analysis and exploration of protein disorder across the tree of life.
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