NetCSSP

NetCSSP predicts contact-dependent secondary structure propensities to identify chameleon sub-sequences that may contribute to amyloid fibril formation.

Key Features:

• CSSP Algorithm Implementation: NetCSSP implements the latest version of the contact-dependent secondary structure propensity (CSSP) algorithm, enabling sensitive and precise calculation of non-native secondary structure propensities.
• Pre-calculated Database: Provides non-native secondary structure propensities for over 1.4 million seven-residue-long fragments derived from Protein Data Bank (PDB) structures.
• Quantitative Mutational Effect Estimation: Enables quantitative estimation of how sequence substitutions affect CSSP values and local secondary structure propensity.
• Chameleon Sub-sequence Identification: Identifies regions with non-native secondary structure propensities that may act as cores for amyloid fibril formation.

Scientific Applications:

• Amyloid Core Identification: Identification of chameleon sub-sequences that may serve as amyloidogenic cores in fibril formation.
• Aggregation Hotspot Analysis: Analysis of local conformational changes and aggregation-prone hotspots in proteins relevant to amyloid diseases.
• Predictive Modeling and Experimental Design: Estimation of mutation-induced changes in secondary structure propensity to inform predictive models and experimental designs.
• Therapeutic Targeting Studies: Support for studies aiming to design therapeutic interventions that target processes involved in amyloid formation.

Methodology:

Calculates CSSP values based on contact-dependent interactions within protein sequences; uses a database of pre-calculated non-native propensities for seven-residue PDB-derived fragments; provides quantitative estimation of mutational impacts on CSSP values.