Kihara Bioinformatics Lab Research Summary 2016
-
Upload
daisuke-kihara -
Category
Science
-
view
319 -
download
1
Transcript of Kihara Bioinformatics Lab Research Summary 2016
![Page 1: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/1.jpg)
1
Daisuke KiharaProfessor of Biological Sciences, Computer Science
Bioinformatics Virtual drug screening Protein structure prediction Structure modeling for electron microscopy data
http://[email protected]:@kiharalab
![Page 2: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/2.jpg)
PL-PatchSurfer2: Molecular Surface-Based Virtual Screening Method
2
Compound LibraryBinding Pocket
Adenosine-binding
(Shin,Christoffer, Wang, Kihara, JCIM, 2016)
Methods Structure EF1% BEDROC
PL-PSurfer2 X-ray 12.86 0.31
TBM 11.76 0.31
Autodock Vina
X-ray 8.63 0.33
TBM 1.68 0.09
DOCK6 X-ray 11.70 0.26
TBM 2.58 0.12
http://kiharalab.org
Benchmark on the DUD dataset
• Performs better than existing methods particularly on computationally modelled target protein structures
![Page 3: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/3.jpg)
Protein Docking
Drug Virtual Screening
Electron Microscopy
Structure Data
Ligand Binding Pocket
Comparison
http://kiharalab.org 3
![Page 4: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/4.jpg)
Protein Function Prediction
4
http://kiharalab.org/pfp_esg.php
http://kiharalab.org
![Page 5: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/5.jpg)
Genome-Scale Detection of Moonlighting Proteins
•Proteins that have two distinct functions in a single chain
•Genome-scale prediction of moonlighting proteins
• 2.7 % of C. elegans, 7.8% of human, and 11.0 % of yeast proteins in their genomes are predicted to be moonlighting proteins
5
(Khan & Kihara, Bioinformatics 2016)
http://kiharalab.org
![Page 6: Kihara Bioinformatics Lab Research Summary 2016](https://reader036.fdocuments.in/reader036/viewer/2022062903/58a8fd391a28ab837c8b6289/html5/thumbnails/6.jpg)
FoldsTksfE
TksfE=)s|p(f
kf
Bjk
Bjiji /|exp(/|exp(
Protein Folding Channel
Consider information theoretic noisy channel that transmit sequence (S) information to protein structures (F, folds)
6
P(fi|sj)
Boltzmann distribution:
(Magner, Szpankowski, Kihara, Scientific Reports, 2015)
http://kiharalab.org