Jpred WS (jabaws)

Jpred WS (jabaws) predicts protein secondary structure and solvent accessibility and performs multiple sequence alignment analyses to support protein structural and functional inference.

Key Features:

• Secondary Structure Prediction: Implements the Jnet algorithm to predict three-state secondary structure elements (α-helices, β-strands, coils) and solvent accessibility from single protein sequences or multiple sequence alignments.
• Multiple Sequence Alignment: Provides MSA generation using Probcons, T-Coffee, Muscle, MAFFT and ClustalW to produce alignments for downstream profile and comparative analyses.
• Integration with Jalview: Exposes MSA and prediction outputs compatible with the Jalview multiple sequence analysis workbench (from version 2.6).
• Parameter Customization: Supports full access to application parameters and named parameter presets plus execution limits via configuration files for tailored analyses.
• JABAWS Web Services: Exposes prediction and alignment algorithms as JABAWS web services for remote execution and integration into external workflows.

Scientific Applications:

• Protein Structure Prediction: Secondary structure and solvent accessibility predictions support inference of protein folding patterns and stability relevant to enzymology and drug design.
• Evolutionary Studies: Multiple sequence alignments enable comparative sequence analysis to assess evolutionary relationships and conservation of structural features.
• Functional Annotation: Structural motif and solvent accessibility information aid annotation of protein sequences with putative functional sites and surface properties.

Methodology:

Uses the Jnet algorithm's three-state model for secondary structure prediction, derives alignment profiles from single sequences or MSAs, employs Probcons, T-Coffee, Muscle, MAFFT and ClustalW for MSA generation, and provides solvent accessibility predictions.