Hh pred

Hh pred

1. HHPred

2. Content Introduction Objectives Input & Output Parameters Methodology Conclusion

3. HHpred is a fast server for remote protein homology detection and structure prediction. Introduction

4. “ HHPred allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD.”

5. Objectives Available on HHPred is a web based tool that can accessed through any web browser. Research Outcome HHpred sensitivity is competitive with the most powerful servers for structure prediction currently available. Analyzes HHPred analyzes the protein homology and predicted structures of proteins.

6. Input The tool requires to prepare or used already existing template protein sequence in FASTA format. It provides the isoforms of the target protein and their accession IDs, in a graphical representation. Output Input & Output

7. Outline of the HHpred algorithm

8. 1st Input Requires to enter query protein in A3M/Clustal/FASTA/Stockholm format. 2nd Parameters Requires to provide MSA generation method, MSA generation iterations, E-value cutoff for MSA generation etc. Parameters

9. Conserved motifs Check for possible conserved motifs. Predictions Verify the predictions experimentally. Check E-value Measures the probability & E-value for query protein. Alignments Check query and template alignments. Top hits Check relationship among top hits. Methodology Secondary structure Check secondary structure similarity.

10. HHpred is a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred sensitivity is competitive with the most powerful servers for structure prediction currently available. Conclusion