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PPT-DB: the protein property prediction and testing database

PPT-DB: the protein property prediction and testing database,10.1093/nar/gkm800,Nucleic Acids Research,David S. Wishart,David Arndt,Mark V. Berjanskii

PPT-DB: the protein property prediction and testing database   (Citations: 8)
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The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. sec- ondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources. PPT- DB is designed to serve two purposes. First it is intended to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or 'derived' protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create. The second role that PPT-DB can play is as a tool for homology- based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence simi- larity search against PPT-DB's extensive collection of proteins with known properties. PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins. Predictions derived from PPT-DB's similarity searches are typically 85-95% correct (for categorical predictions, such as sec- ondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http:// www.pptdb.ca
Journal: Nucleic Acids Research - NAR , vol. 36, no. Database-I, pp. 222-229, 2008
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    • ...Many studies have been conducted to estimate protein folding rates based on either experimental protein structural information [4-7] or protein homology sequence searches using databases [8]...
    • ...A few applications and web servers have been developed for protein rate predictions, such as FOLD-RATE [23], and PPT-DB [8], but not yet for fold kinetic classification...
    • ...It has been used by many researchers as multi-state folder [14,18,19,36], but later it was shown experimentally to be a two-state folder [8,37]...

    Guan Ning Linet al. SeqRate: sequence-based protein folding type classification and rates ...

    • ...These include Proteus2 (18) to perform structural modeling and energy refinement, PREDITOR (12) to calculate torsion angles (from NOEs or chemical shifts), PPT-DB (19) for comparative modeling and alignment and CS23D (10) to calculate protein structures from chemical shifts...
    • ...Briefly, the sequence is searched against a non-redundant database of PDB sequences and secondary structures from PPT-DB (19) using BLAST (25) with a sliding length-dependent Expect cutoff, ranging from 101 (for <11 residues) to 105 (for >50 residues)...
    • ...As with ‘Scenario (a)’, the sequence is searched against a nonredundant database of PDB sequences and secondary structures from PPT-DB (19) using BLAST (25) with a sliding length-dependent Expect cutoff, ranging from 101 (for <11 residues) to 105 (for >50 residues)...

    Mark V. Berjanskiiet al. GeNMR: a web server for rapid NMR-based protein structure determinatio...

    • ...Many studies have been conducted to estimate protein folding rates based on either experimental protein structural information [2-4] or protein homology sequence searches using databases [5]...
    • ...A few applications and web servers have been developed for protein rate predictions, such as FOLD-RATE [13], and PPT-DB [5], but only one server K-Fold [4] for fold kinetic classification...
    • ...Chromosomal protein Ubiquitin (PDB ID: 1UBQ) has a sequence length of 76 amino acids and experimental folding rate of 7.3 (in natural-base logarithm scale) in the unit of sec -1 . It has been used by many researchers as multi-state folder [7,11], but later it was shown experimentally to be a two-state folder [5]...

    Guan Ning Linet al. Sequence-Based Prediction of Protein Folding Rates Using Contacts, Sec...

    • ...The sequence file is searched against a nonredundant database of PDB sequences and secondary structures from PPT-DB (21) using BLAST (22) with a length-dependent Expect cutoff, ranging from 101 (for <11 residues) to 105 (for >50 residues)...
    • ...THRIFTY is also used to perform a secondary structure alignment between the secondary structure of the query protein (calculated by CSI) and a large database of known protein secondary structures maintained at the PPT-DB (21)...

    David S. Wishartet al. CS23D: a web server for rapid protein structure generation using NMR c...

    • ...This step is followed by BLASTing the query protein against a database of 2587 proteins with known signal peptides obtained from the PPT-DB (22)...
    • ...Training and testing of the algorithms was conducted using the relevant transmembrane PPT-DB databases (22)...

    Scott Montgomerieet al. PROTEUS2: a web server for comprehensive protein structure prediction ...

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