P3Fold

P3Fold predicts protein folding routes and residue contacts to elucidate how polypeptide chains attain their native three-dimensional structures using statistical and evolutionary information.

Key Features:

• Coarse-Grained Modeling: Employs coarse-grained modeling techniques to simplify molecular interactions and support residue-contact prediction.
• Combinatorial Evaluation of Folding Routes: Utilizes combinatorial schemes to rapidly evaluate potential folding routes for protein sequences.
• Integration of Statistical and Evolutionary Data: Integrates statistical models with evolutionary information to inform predictions of folding routes and residue contacts.
• Residue Contact Prediction: Predicts residue contacts within proteins to inform identification of folding pathways and intermediates.

Scientific Applications:

• Protein family analyses: Supports both large-scale and short-scale experiments on protein families to compare folding behaviors.
• Human proteome studies: Enables analysis of the human proteome to uncover conservation and variation of structural intermediates across proteins.
• Evolutionary biology and structural bioinformatics: Applies to studies of evolutionary constraints on folding and structural bioinformatics investigations.
• Molecular dynamics and folding intermediates: Facilitates investigation of folding intermediates and aspects of molecular dynamics related to folding routes.

Methodology:

Combines coarse-grained modeling with statistical models and evolutionary information to predict residue contacts and employs combinatorial schemes to evaluate possible folding routes.