PrISM

PrISM provides integrated protein sequence and structure analysis, alignment, modeling, and assessment to support comparative modeling and protein structure prediction.

Key Features:

• Integrated modules: Alignment, modeling, and assessment modules are combined to perform protein sequence and structure analysis and modeling.
• Complex sequence alignment handling: Capable of handling complex sequence alignment tasks that are crucial for accurate protein structure prediction.
• Multiple alignment methods and parameter sets: Incorporates multiple alignment algorithms and configurable parameter sets for alignment generation.
• Model ranking system: Uses a model ranking system to evaluate and inform selection among generated alignments and models.
• Advanced sequence-template alignment procedures: Implements sequence-template alignment procedures that can outperform standard pairwise dynamic programming for difficult query–template pairs.
• Comparative modeling support: Tailored for comparative modeling scenarios involving structurally related templates and target sequences.
• Community benchmarking usage: Applied to predict models for CASP3 target sequences, demonstrating use in community structure-prediction experiments.

Scientific Applications:

• Protein sequence and structure analysis: Analysis of protein sequences and structural models for research in structural bioinformatics.
• Comparative modeling: Generation and assessment of comparative models using related structural templates.
• Alignment of remotely related sequences: Addressing alignment challenges for remotely related query–template pairs that involve extensive insertions and deletions.
• Model evaluation and selection: Ranking and selection of models produced from multiple alignment and modeling protocols.
• Structure prediction benchmarking: Application in community experiments such as CASP3 for predicting target structures.

Methodology:

Combines multiple alignment methods with configurable parameter sets, a model ranking system, advanced sequence–template alignment procedures as alternatives to pairwise dynamic programming, and integrated alignment, modeling, and assessment modules.