SCRATCH

SCRATCH predicts protein tertiary structures and multiple residue- and domain-level structural features from amino acid sequences for use in structural and functional analyses.

Key Features:

• Secondary Structure Prediction: Predicts secondary structure elements such as alpha-helices and beta-sheets from amino acid sequences.
• Relative Solvent Accessibility: Predicts residue-level relative solvent accessibility to identify surface-exposed regions.
• Disordered Regions Identification: Identifies regions lacking fixed three-dimensional structure, enabling study of intrinsically disordered proteins.
• Domain Prediction: Predicts structural domains within protein sequences to inform functional and evolutionary analyses.
• Disulfide Bridge Prediction: Predicts potential disulfide bonds between cysteine residues that stabilize protein structures.
• Single Mutation Stability Analysis: Assesses the impact of single amino acid substitutions on protein stability.
• Residue Contacts Prediction: Predicts average residue contacts and specific residue–residue interactions to map intra-protein contacts.
• Tertiary Structure Prediction: Predicts three-dimensional tertiary structures of proteins from sequence.

Scientific Applications:

• Structural Biology: Provides predicted tertiary and secondary structures for interpretation and experimental planning in structural biology.
• Molecular Modeling: Supplies secondary structure, contact, solvent accessibility, and disulfide information as restraints and features for molecular modeling and structure refinement.
• Drug Design: Informs drug design by identifying structural features, potential interaction sites, and stability effects of mutations.
• Study of Intrinsically Disordered Proteins: Enables analysis of disordered regions and their functional roles.
• Protein Engineering and Mutational Analysis: Supports protein engineering and assessment of disease-related or designed single amino acid mutations via stability predictions.
• Protein–Protein Interaction Mapping: Informs mapping of intra-protein contacts and potential interaction interfaces through residue contact and solvent accessibility predictions.
• Domain Function and Evolution: Assists functional annotation and evolutionary studies through domain prediction.

Methodology:

Uses a suite of sequence-based predictors to generate secondary structure, relative solvent accessibility, disorder, domain assignments, disulfide bridge predictions, single-mutation stability estimates, residue contact maps, and tertiary structure models from amino acid sequences.