Protinfo

Protinfo predicts protein tertiary structures from amino acid sequences using comparative and de novo modeling to produce atomic coordinates for structural analysis.

Key Features:

• Sequence input and atomic coordinate output: Accepts protein sequences and generates atomic coordinates representing predicted tertiary structures.
• Comparative Modeling: Aligns target sequences with known protein structures to infer three-dimensional structure based on evolutionary relationships.
• De Novo Modeling: Predicts structures without homologous templates using physicochemical properties of amino acids and principles of protein folding.
• CASP-evaluated Algorithms: Incorporates enhanced back-end algorithms that have been evaluated in Critical Assessment of Protein Structure Prediction (CASP) meetings.
• Secondary Structure Assignment via NMR and Neural Networks: Integrates NMR chemical shift data with neural networks to improve secondary structure predictions.

Scientific Applications:

• Hypothesis generation and testing: Provides structural models to support biological hypothesis generation and experimental testing.
• Experimental design: Informs experimental design by supplying predicted tertiary and secondary structural information.
• Function and interaction analysis: Supports analyses of protein function and protein–protein or protein–ligand interactions.
• Protein design: Assists in designing novel proteins with specified structural characteristics.

Methodology:

Comparative modeling via sequence–structure alignment to known templates; de novo modeling based on amino acid physicochemical properties and folding principles; use of enhanced algorithms benchmarked in CASP; neural networks integrating NMR chemical shift data for secondary structure assignment.