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Protein Interactions in (and) Disease Maricel Kann (NIH), Yanay Ofran (Columbia), Marco Punta (Columbia), and Predrag R PowerPoint Presentation
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Protein Interactions in (and) Disease Maricel Kann (NIH), Yanay Ofran (Columbia), Marco Punta (Columbia), and Predrag Radivojac (Indiana). Protein Interactions. Protein and diseases. LINKING INTERACTIONS TO DISEASE Analyzing interactions. Protein Interactions. Protein and diseases.

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Presentation Transcript
slide1

Protein Interactions in (and) Disease

Maricel Kann (NIH), Yanay Ofran (Columbia),

Marco Punta (Columbia), and Predrag Radivojac (Indiana)

slide2

Protein Interactions

Protein and diseases

LINKING INTERACTIONS TO DISEASE

Analyzing interactions

slide3

Protein Interactions

Protein and diseases

LINKING INTERACTIONS TO DISEASE

Analyzing interactions

slide4

Protein Interactions

Protein and diseases

LINKING INTERACTIONS TO DISEASE

Analyzing interactions

slide5

Detecting protein-protein interactions

High-throughput

Two-hybrid systems Fields FEBS (2005) 262:5391-5399 - Review

Mass SpectrometryMann et al. (2001) Rev Biochem. 70:437-473 -Review

MicroarraysESPEJO et al. (2002) Biochem. J. 367 (697–702)

Single protein

Molecular biology

slide6

Expanding protein-protein interaction

DATAbases

Sequence similarity

Structural similarity

De NOVO

slide7

From:

A Protein Interaction Map of Drosophila melanogaster

Giot,Rothberg et al. Science 302, 1727-1136 (2003)

interaction map

slide8

Expanding protein-protein interaction

DATAbases

Sequence similarity

Structural similarity

De NOVO

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction

Rohit Singh, Jinbo Xu, and Bonnie Berger

slide9

Linking protein-protein interactions

to disease

Online Mendelian Inheritance in Man (OMIM)

McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National

Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000.

World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/

Protein-Disease Database (PDD)

Maintained by NCI

PharmGKB

Thorn, Klein and Altman (2005) Methods Mol Biol., 311:179-91.

slide10

From:

Towards a proteome-scale map of the human protein–protein interaction network

Rual, Vidal et al. Nature 437, 1173-1178 (2005)

slide11

From:

Towards a proteome-scale map of the human protein–protein interaction network

Rual, Vidal et al. Nature 437, 1173-1178 (2005)

Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome Data

Jake Yue Chen, Changyu Shen, and Andrey Y. Sivachenko

Discovering Regulated Networks During HIV-1 Latency and Reactivation

Sourav Bandyopadhyay, Ryan Kelley, and Trey Ideker

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction

Rohit Singh, Jinbo Xu, and Bonnie Berger

slide12

Predicting and analyzing

Protein interaction regions

Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins

Yuzhen Ye, Zhanwen Li, and Adam Godzik

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and RNA Binding

Sites in Rev Proteins of HIV-1 and EIAV Agree with Experimental Data

Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter,

Vasant Honavar, and Drena Dobbs

Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction

of Binding Affinities of Protein-DNA Interactions

Sumedha Gunewardena and Zhaolei Zhang

Improving Computational Predictions of Cis- Regulatory Binding Sites

Mark Robinson, Yi Sun, Rene Te Boekhorst, Paul Kaye, Rod Adams, Neil Davey, and Alistair G. Rust

slide13

What is next?

Modeling biological processes

Modeling and Simulation with Hybrid Functional Petri Nets of the Role of Interleukin-6 in

Human Early Haematopoiesis

Sylvie Troncale, Fariza Tahi, David Campard, Jean-Pierre Vannier, and Janine Guespin

slide14

Protein Interactions in Disease

8:50-9:10         Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins

Yuzhen Ye, Zhanwen Li, and Adam Godzik

9:10-9:30         Mining Alzheimer Disease Relevant Proteins from Integrated Protein Interactome

DataYue Chen, Shen, and Sivachenko

9:30-9:50         Modeling and Simulation with Hybrid Functional Petri Nets of the Role of

Interleukin-6 in Human Early Haematopoies

Troncale, Tahi, Campard, Vannier, and Guespin

9:50-10:10       Identifying Interaction Sites in “Recalcitrant” Proteins: Predicted Protein and

RNA Binding Sites in Rev Proteins of HIV and EIAV Agree with Experimental Data

Terribilini, Lee, Yan, Jernigan, Carpenter, Honavar, and Dobbs

10:10-10:30     Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction

Singh, Xu, and Berger

10:30-10:50     Discovering Regulated Networks During HIV-1 Latency and Reactivation

Bandyopadhyay, Kelley, and Ideker

10:50-11:30    Coffee Break

11:30-1:00       Discussion Session: Protein Interactions in Disease