Canavan Disease: Task 06 - Protein Structure Prediction

Dataset

To gain the HRas multiple sequence alignment the instructions were followed and the full MSA provided by Pfam (PF00071) was downloaded and used for further calculations and statistics. Searching for a multiple sequence alignment for ASPA/ACY2 in Pfam revealed that the two criteria to gain meaningful insights out of the calculations of freecontact, evcouplings and evfold, namely over 1000 sequences in the MSA and large parts of the reference sequence are contained in the MSA, are satisfied. The multiple sequence alignment for the protein family containing ASPA (PF04952) includes 2822 sequences and the region of ASPA that is used in the MSA spans from position 10 to 301 with ASPA having a total length of 313 amino acids. Hence the Pfam MSA is regarded as viable input for the following calculations.

Tasks

• Link to Task 01: Canavan Disease
• Link to Task 02: Alignments
• Link to Task 03: Sequence-based Predictions
• Link to Task 04: Structural Alignments
• Link to Task 05: Homology Modelling
• Link to Task 06: Protein Structure Prediction from Evolutionary Sequence Variation
• Link to Task 07: Researching SNPs
• Link to Task 08: Sequence-based Mutation Analysis
• Link to Task 09: Structure-based Mutation Analysis
• Link to Task 10: Normal Mode Analysis
• Link to Task 11: Molecular Dynamics Simulation