일시: 2015년 3월 12일 목요일 오전 11시

연사: 석 차 옥 교수님 (서울대학교 자연과학대학 화학부)

장소: 서울대학교 25동 411호

Title: Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs

Abstract:

Recently developed GALAXY protein modeling programs are introduced. The GALAXY package consists of the template-based modeling program GalaxyTBM, the loop/terminus modeling program GalaxyLoop, the model refinement program GalaxyRefine, the homo-oligomer prediction program GalaxyGemini, the ligand binding site prediction program GalaxySite, the protein-ligand docking program GalaxyDock, and the protein-protein docking program GalaxyPPDock. These programs have been tested with some success in community-wide competitions Critical Assessment of Techniques for Protein Structure Prediction (CASP) and Critical Assessment of PRediction of Interactions (CAPRI). For the development of these programs, modeling problems have been posed as global optimization problems of designed energy functions. The free energy functions of GALAXY have been carefully designed by combining physical chemistry principles and structure and sequence information. Efficient conformational search methods such as conformational space annealing and triaxial loop closure have been employed. Freely accessible web servers of the modeling programs are available at　http://galaxy.seoklab.org, and some programs can be downloaded from　http://galaxy.seoklab.org/softwares.

Bio:

EDUCATION
1998　Ph.D.　Chemistry, University of Chicago, Chicago, USA　
1993　B.S.　Chemistry, Seoul National University, Seoul, Korea

PROFESSIONAL EXPERIENCES
Sep 2013 –　Professor, Chemistry, Seoul National University, Korea
Aug 2008 – Aug 2013　Associate Professor, Chemistry, Seoul National University, Korea
Apr 2008 – Mar 2010　Affiliate Professor, Computational Science, Korea Institute for Advanced Study
Aug 2004 – Jul 2008　Assistant Professor, Chemistry, Seoul National University, Korea
Jun 2000 – Jul 2004　Research Associate, Pharmaceutical Chemistry, University of California, San Francisco, USA
Jan 2000 – May 2000　Research Associate, Chemistry, MIT, Cambridge, USA
Jan 1999 – Dec 1999　Research Associate, Chemistry, University of Chicago, Chicago, USA

HONORS
2013　Excellence in Research Award, College of Natural Sciences, Seoul National University
2008　Teaching Award, College of Natural Sciences, Seoul National University

RESEARCH INTERESTS
Computational study of structure and function of biomolecules:
Protein structure prediction, Protein loop modeling, Protein-ligand docking,　
Protein-protein docking, Membrane protein structure and function,

PROGRAMS AND WEB SERVERS DEVELOPED BY SEOK LAB
　GALAXY protein modeling program package for protein structure prediction and refinement, protein-ligand docking, and protein-protein docking

　GalaxyWEB (http://galaxy.seoklab.org/)
•　GalaxyTBM: Protein structure prediction from sequence by template-based modeling
•　GalaxyLoop: Modeling of loop and/or terminus regions specified by user
•　GalaxyRefine: Refinement of model structure provided by user
•　GalaxySite: Ligand binding site prediction from a given protein structure (experimental or model)
•　GalaxyGemini: Protein homo-oligomer structure prediction from a given protein monomer structure (experimental or model)

SELECTED PUBLICATIONS
1.　L. Heo, W. -H. Shin, M. S. Lee, and C. Seok*, GalaxySite: Ligand-binding site prediction by using molecular docking, Nucleic Acids Res. 42 (W1), W210-W214 (2014).　
2.　W. -H. Shin, G. R. Lee, L. Heo, H. Lee, and C. Seok*, Prediction of Protein Structure and Interaction by GALAXY protein modeling programs, Bio Design, 2 (1), 1-11 (2014).　
3.　W. -H. Shin, J. -K. Kim, D. -S. Kim*, and C. Seok*, GalaxyDock2: Protein-ligand docking using beta-complex and global optimization, J. Comput. Chem. 34 (30), 2647-2656 (2013). (Inside Cover)
4.　L. Heo, H. Park, and C. Seok*, GalaxyRefine: Protein structure refinement driven by side-chain repacking, Nucleic Acids Res. 41 (W1), W384-W388 (2013).　
5.　H. Lee, H. Park, J. Ko, and C. Seok*, GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity, Bioinformatics, 29 (8), 1078-1080 (2013).
6.　W. -H. Shin and C. Seok*, GalaxyDock: Protein-ligand docking with flexible protein side-chains, J. Chem. Inf. Model, 52 (12), 3225-3232 (2012).　
7.　J. Ko, H. Park, and C. Seok*, GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions, BMC Bioinformatics, 13, 198 (2012).　
8.　J. Ko, H. Park, L. Heo, and C. Seok*, GalaxyWEB server for protein structure prediction and refinement, Nucleic Acids Res. 40 (W1), W294-W297 (2012).　
9.　H. Park and C. Seok*, Refinement of unreliable local regions in template-based protein models, Proteins: Structure, Function, and Bioinformatics, 80 (8), 1974-1986 (2012).
10.　W. Shin, L. Heo, J. Lee, J. Ko, C. Seok*, and J. Lee*, LigDockCSA: protein-ligand docking using conformational space annealing, J. Comput. Chem. 32 (15), 3226-3232, (2011).　
11.　H. Park, J. Ko, K. Joo, J. Lee, C. Seok*, and J. Lee*, Refinement of protein termini in template-based modeling using conformational space annealing, Proteins: Structure, Function, and Bioinformatics, 79, 2725-2734 (2011).　
12.　J. Ko, D. Lee, H. Park, E. A. Coutsias, J. Lee*, and C. Seok*, The FALC-Loop web server for protein loop modeling, Nucleic Acids Res. 39, W210-W214 (2011).　
13.　J. Lee*, D. Lee, H. Park, E. A. Coutsias, and C. Seok*, Protein loop modeling by using fragment assembly and analytical loop closure, Proteins: Structure, Function, and Bioinformatics, 78, 3428-3436 (2010).　
14.　J. Lee, Y. -G. Kim, K. K. Kim, and C. Seok*, Transition between B-DNA and Z-DNA: Free Energy Landscape for the B-Z Junction Propagation, J. Phys. Chem. B, 114, 9872-9881 (2010).　
15.　J. Lee, J. Kim, and C. Seok*, Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: A molecular dynamics simulation study, J. Phys. Chem. B, 114, 7662-7671 (2010).　
16.　J. Lee and C. Seok*, A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect, Proteins: Structure, Function, and Bioinformatics, 70, 1074-1083 (2008).
17.　C. Seok* and E. A. Coutsias*, Efficiency of rotational operators for geometric manipulation of chain molecules, Bull. Korean Chem. Soc. 28, 1705 (2007).　
18.　E. A. Coutsias, C. Seok*, and K. A. Dill, Using Quaternions to Calculate RMSD, J. Comput. Chem. 25, 1849 (2004).
19.　E. A. Coutsias, C. Seok*, M. P. Jacobson, and K. A. Dill, A Kinematic View of Loop Closure, J. Comput. Chem. 25, 510-528 (2004).　
20.　C. Seok, J. B. Rosen, J. D. Chodera, and K. A. Dill, MOPED: Method for Optimizing Physical Energy parameters using Decoys, J. Comput. Chem. 24, 89 (2003).