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. phenome-interactome. network of protein complexes implicated in genetic disorders. Kasper . Lage. , E . Olof. . Karlberg. , . Zenia. M . Størling. , . Páll. Í . Ólason. , Anders G Pedersen, Olga . Usman Roshan. BNFO 236. Gap penalties. How do we pick gap parameters to produce meaningful protein sequence alignments?. We use “true” alignments created manually (with some computational input) and with structure information. 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?. Welkin Pope. SEA-PHAGES Bioinformatics Workshop, . 2016. Virion structural and assembly genes. , i.e. those encoding proteins that are either components of virion particles or assist in their formation. These include genes encoding the . N.N. (GI/MR/M) / N.N. (GI/MR/M). Introduction. bbb. Figure. . 1. Nucleic Acid – Protein Interaction . DataBase. . Figure. 2 . SCOP . family. . characteristic. . Figure. . 3 . Classification of protein-DNA interactions. 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. Md. . Mahmudul. . Hasan. and Tamer . Kahveci. University of Florida. Global alignment. R8. R2. R1. R3. R4. R5. R6. R7. R7. R2. R1. R3. R4. R5. R6. Network-1. Network-2. Alignment. Global . alignment . 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. 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 . Hsin. -Yu Chang. www.ebi.ac.uk. Classifying . proteins into families and . identifying . protein homologues can help scientists . to . characterise. unknown proteins. . . . Greider. and Blackburn discovered telomerase in 1984 and were awarded Nobel prize in 2009. Which model organism they used for this study ? . Post-Doctoral Fellow. Ochman. Lab. Global . vs. Local Alignments. Global . . The global approach is useful when you are comparing a small group of sequences, but becomes become computationally expensive as the number of sequence in the comparison increases. . pair-wise alignment. × . multiple . sequence . alignment. Flavors of sequence alignment. global alignment . × . local alignment. global. local. align entire sequence. stretches of sequence with the highest density of matches . . Arzucan . Özgür. Bilgisayar. . Mühendisliği. . Bölümü. Boğaziçi. . Üniversitesi. Karmaşık Sistemler ve Veri Bilimi . Çalıştayı. . 04.05.2019. arzucan.ozgur@boun.edu.tr. General Research Areas. . in . cancer. . research. Borbála Kovács MD., PhD . student. Supervisor. : Prof. Peter Csermely. About. . cancer. Cancer therapeutics currently have . the lowest clinical trial success rate of all major diseases. .