http://www.sienabiografix.it/index_edu.php Protein structure prediction Start End Uniprot Blast Clustalo Modeler Mail: 29/01/2015 Prof. Neri Niccolai [email protected] Simone Gardini [email protected] Protein structure prediction 1. Modeling by homology 2. Ab initio 3. Fold Recognition Flowchart modeling of proteins Protein Sequence Experimental Data MSA Research in databases Assigning domains Homologous protein in the PDB database? Secondary structure prediction NO YES Analysis of the family fold Alignment of secondary structures Homology modeling 3D Model of Protein Prediction Fold Alignment sequence to structure. YES Was predicted a fold? NO Tertiary structure prediction Secondary structure prediction Why predict the secondary structure of proteins? • To study the relationship between structure and function. • To study the molecular phylogeny. • To determine the relationship between proteins with low sequence similarity. • For the design of new proteins and mutants. • For the prediction of the tertiary structure. • To choose the best alignment for the Homology Modeling. JPRED3 http://www.compbio.dundee.ac.uk/www-jpred/ JPRED3 http://www.compbio.dundee.ac.uk/www-jpred/ Choose file MAX 800 AA JPRED3 http://www.compbio.dundee.ac.uk/www-jpred/ JPRED3 JPRED3 JPRED3 JPRED3 What are do the characters 'E', 'H', 'B' and '-' represent in the prediction? They represent extended (E), helical (H) and other (-) types of secondary structure respectively. In the solvent accessibility predictions they represent buried (B) and exposed (-) for each of the 0%, 5% and 25% solvent accessibility cut-offs. Questions!!!! • From UniProt take Fasta sequence of Bik Protein Name: Bik ; Organism: Homo sapiens • Use the tool jpred3 with the query sequence • Analyze result Tertiary structure prediction Homology Modeling HHpred Paste query sequence HHpred HHpred HHpred HHpred HHpred HHpred Modeller http://salilab.org/modeller/ HHpred-MSA 1. 2. Modeller Modeller Modeller registration http://salilab.org/modeller/registration.html Modeller Questions!!!! • Try to build a model for the query sequence, write all the selected passages. Questions!! • Use jpred3, hhpred and modeler to build a model for rna pol ebola. • Remember that the sequence is very long, so you'll have to split the sequence. • When you have finished writing the report. • Good job.