PPT-PINALOG Protein Interaction Network Alignment

and its implication in function prediction and complex detection Hang Phan Prof Michael JE Sternberg Division of Molecular Biosciences Imperial College London PhD Research Day April 1 st 2011. CS/. BioE. 598. Tandy Warnow. Alignment Error/Accuracy. SP-FN: percentage of homologies in the true alignment that are *not* recovered. SP-FP: percentage of homologies in the estimated alignment that are false. Authors: Jamie Snider, Max . Kotlyar. , . Punit. . Saraon. , . Zhong. Yao, Igor . Jurisica. and Igor . Stagljar. Published: December 2015, Molecular Systems Biology. Presentation Outline. Why are Protein-Protein Interactions (PPIs) Important?. Xuhua Xia. xxia@uottawa.ca. http://dambe.bio.uottawa.ca. Xuhua Xia. Slide . 2. Normal and Thalassemia HBb. Are the two genes homologous?. What evolutionary change can you infer from the alignment? . What is the consequence of the evolutionary change?. with. PASTA. Michael Nute. Austin, TX. June 17, 2016. Agenda. Quick recap of PASTA Algorithm. Run the GUI. Explore GUI options and what they do in terms of PASTA. Run a test alignment. Explore PASTA outputs and diagnostics. By: Z. S. . Rezaei. Structural comparison. Structural alignment. spectrum. of structural alignment methods. The properties of output. Types of comparison. Algorithmic complexity. Representation of structures. . You have learned about:. Data & databases. Tools . Amino Acids. Protein Structure. Today we will discuss: . Aligning sequences. After this: . You know how to perform structural alignments. Interactions. June 6, 2017. Why PPI?. Protein-protein interactions determine outcome of most cellular processes. Proteins which are close homologues often interact in the same way. Protein-protein interactions place evolutionary constraints on protein sequence and structural divergence. Cytochrome and Photosystem I . W. Chen, A. . Sekmen. , . B. Bruce, K. . Nguya. , . P. Mishra, L. . . Emujakporue. ,. K. . Wehbi. . Computer Science, . Tennessee State University . Biochemistry & Cellular & Molecular Biology, . by . Sadhana S. definition. Protein structure prediction/protein . modelling. is the prediction of the three-dimensional structure of protein from its amino acid sequence. i.e., the prediction of its folding & its. In a day and age where people have busier lifestyles, where obesity is becoming a trend, and homes becoming smaller – manufacturers have created an empire surrounding quick and easy meals, snacks, and even drinks. More people prefer instant gratification, which led to wanting things done in an instant – instant messaging, instant coffee, instant noodles, and even instant meals! Tandy . Warnow. Joint with Mike . Nute. and Ehsan Saleh. https://. www.biorxiv.org. /content/early/2018/04/20/304659. Performance Study on bioRxiv . Goal: Evaluate . Bali-Phy. (Redelings and Suchard) on both biological and simulated datasets, in comparison to leading alignment methods on small protein sequence datasets . Jia. -Ming Chang, Paolo Di . Tommaso. , and Cedric . Notredame. TCS. : A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree . reconstruction, . Automated Mode SWISS MODEL. Alignment Mode SWISS MODEL. PyMol tutorial. Structural comparison. PyMol. Model assessment. MolProbity. Model assessment. MolProbity. find homologous sequences - . BLAST. Steve Jupe. Motivation for Pathway and Network Analysis in Cancer. “. Exclusivity principle. ”. in cancer.. once a gene is mutated in a pathway, the selective growth advantage incurred by a second mutated gene in the same pathway is minimal..