Chaok Seok: search on Z-Library

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1

Using quaternions to calculate RMSD

Evangelos A. Coutsias, Chaok Seok, Ken A. Dill

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 135 KB

english, 2004

2

From Single Structures to Ensembles: Application of the Galaxy Program Suite to Ubiquitin, Cyclophilin a and PTP1B

Rie Lee, Gyu, Seok, Chaok, Buck, Matthias

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 40 KB

english, 2018

3

Template-Based Protein Modeling using Global and Local Templates

Ko, Junsu, Park, Hahnbeom, Seok, Chaok, Lee, Jooyoung

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 40 KB

english, 2010

4

Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation

Lee, Juyong, Kim, Yang-Gyun, Kim, Kyeong Kyu, Seok, Chaok

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 4.66 MB

english, 2010

5

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

Chodera, John D., Swope, William C., Pitera, Jed W., Seok, Chaok, Dill, Ken A.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 165 KB

english, 2007

6

GalaxySagittarius: Structure- and similarity-based prediction of protein targets for drug-like compounds

Yang, Jinsol, Kwon, Sohee, Bae, Sang-Hun, Park, Kyoung Mii, Yoon, Changsik, Lee, Ji-Hyun, Seok, Chaok

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 437 KB

2020

7

Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling

Kim, Gijeong, Yang, Jinsol, Jang, Juwon, Choi, Jin-Seok, Roe, Andrew J., Byron, Olwyn, Seok, Chaok, Song, Ji-Joon

Journal:

Communications Biology

Year:

2020

File:

PDF, 2.83 MB

2020

8

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4

Xu, Qifang, Tang, Qingling, Katsonis, Panagiotis, Lichtarge, Olivier, Jones, David, Bovo, Samuele, Babbi, Giulia, Martelli, Pier L., Casadio, Rita, Lee, Gyu Rie, Seok, Chaok, Fenton, Aron W., Dunbrack

Journal:

Year:

2017

Language:

english

File:

PDF, 1.06 MB

english, 2017

9

Tribute to Ken A. Dill

Hribar-Lee, Barbara, Seok, Chaok, Coutsias, Evangelos, Lukšič, Miha

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 3.36 MB

english, 2018

10

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Woo, Hyeonuk, Park, Sang-Jun, Choi, Yeol Kyo, Park, Taeyong, Tanveer, Maham, Cao, Yiwei, Kern, Nathan R., Lee, Jumin, Yeom, Min Sun, Croll, Tristan Ian, Seok, Chaok, Im, Wonpil

Journal:

Journal of Physical Chemistry B

Year:

2020

File:

PDF, 1.44 MB

2020

11

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

Junsu Ko, Hahnbeom Park, Chaok Seok

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 286 KB

english, 2012

12

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

Lee, Gyu Rie, Heo, Lim, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

13

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

Baek, Minkyung, Park, Taeyong, Heo, Lim, Park, Chiwook, Seok, Chaok

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.34 MB

english, 2017

14

Improving Docking Performance of Large Flexible Ligands using Hot Spot Information Predicted by Fragment Docking

Baek, Minkyung, Seok, Chaok

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 46 KB

english, 2018

15

Phase transitions in AgI

Seok, Chaok, Oxtoby, David W.

Journal:

Physical Review B

Year:

1997

Language:

english

File:

PDF, 169 KB

english, 1997

16

Bulk and surface nucleation of the order-disorder transition in

Seok, Chaok, Oxtoby, David W

Journal:

Journal of Physics Condensed Matter

Year:

1998

Language:

english

File:

PDF, 120 KB

english, 1998

17

Cover Image, Volume 85, Issue 3

Lee, Hasup, Baek, Minkyung, Lee, Gyu Rie, Park, Sangwoo, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

File:

PDF, 2.02 MB

2017

18

GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility

Yang, Jinsol, Baek, Minkyung, Seok, Chaok

Journal:

Journal of Computational Chemistry

Year:

2019

File:

PDF, 1.94 MB

2019

19

New molecular interaction of IIA Ntr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

Kim, Mi-Sun, Lee, Hasup, Heo, Lim, Lim, Areum, Seok, Chaok, Shin, Dong Hae

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.82 MB

english, 2013

20

A kinematic view of loop closure

Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 443 KB

english, 2004

21

Polymer blends near patterned surfaces

Seok, Chaok, Freed, Karl F., Szleifer, Igal

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 385 KB

english, 2000

22

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

Lee, Hui Sun, Seok, Chaok, Im, Wonpil

Journal:

Journal of Chemical Theory and Computation

Year:

2015

Language:

english

File:

PDF, 2.98 MB

english, 2015

23

Refinement of unreliable local regions in template-based protein models

Hahnbeom Park, Chaok Seok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 2.20 MB

english, 2012

24

Switchable Nanoporous Sheets by the Aqueous Self-Assembly of Aromatic Macrobicycles

Kim, Yongju, Shin, Suyong, Kim, Taehoon, Lee, Dongseon, Seok, Chaok, Lee, Myongsoo

Journal:

Angewandte Chemie International Edition

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

25

Heterogeneous nucleation of a monomer gas on a growing gas-phase polymer

Seok, Chaok, Oxtoby, David W.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 350 KB

english, 1999

26

Nucleation in n-alkanes: A density-functional approach

Seok, Chaok, Oxtoby, David W.

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 409 KB

english, 1998

27

MOPED: Method for optimizing physical energy parameters using decoys

Chaok Seok, J. B. Rosen, John D. Chodera, Ken A. Dill

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 145 KB

english, 2003

28

A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect

Juyong Lee, Chaok Seok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 250 KB

english, 2008

29

Protein loop modeling by using fragment assembly and analytical loop closure

Julian Lee, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Chaok Seok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 178 KB

english, 2010

30

Refinement of protein termini in template-based modeling using conformational space annealing

Hahnbeom Park, Junsu Ko, Keehyoung Joo, Julian Lee, Chaok Seok, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 950 KB

english, 2011

31

GALAXYDock: Docking Ligands to Receptor Proteins with Selected Flexible Side-Chains

Shin, Woong-Hee, Seok, Chaok

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

32

Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

Heo, Lim, Cho, Yoo-Bok, Lee, Myeong Sup, Roe, Jung-Hye, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 578 KB

english, 2013

33

Absolute binding free energies for octa-acids and guests in SAMPL5

Tofoleanu, Florentina, Lee, Juyong, Pickard IV, Frank C., König, Gerhard, Huang, Jing, Baek, Minkyung, Seok, Chaok, Brooks, Bernard R.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

34

Biophysical and functional characterization of Norrin signaling through Frizzled4

Bang, Injin, Kim, Hee Ryung, Beaven, Andrew H., Kim, Jinuk, Ko, Seung-Bum, Lee, Gyu Rie, Lee, Hasup, Im, Wonpil, Seok, Chaok, Chung, Ka Young, Choi, Hee-Jung

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 1.35 MB

english, 2018

35

Structure Prediction of Biological Assemblies using GALAXY in CAPRI Rounds 38‐45

Park, Taeyong, Woo, Hyeonuk, Baek, Minkyung, Yang, Jinsol, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2019

Language:

english

File:

PDF, 1.62 MB

english, 2019

36

Parameter optimization for the Gaussian model of protein folding

Albert Erkip, Burak Erman, Chaok Seok, Ken Dill

Journal:

Year:

2002

Language:

english

File:

PDF, 1005 KB

english, 2002

37

Computational Modeling of the Binding Mode of Transcription Activator-Like Effectors to DNA

Lee, Dongseon, Shin, Woong-Hee, Seok, Chaok

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

38

GalaxyDock2: Protein-ligand docking using beta-complex and global optimization

Shin, Woong-Hee, Kim, Jae-Kwan, Kim, Deok-Soo, Seok, Chaok

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 620 KB

english, 2013

39

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors

Won, Jonghun, Lee, Gyu Rie, Park, Hahnbeom, Seok, Chaok

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 1.01 MB

english, 2018

40

Prediction of protein oligomer structures using GALAXY in CASP13

Baek, Minkyung, Park, Taeyong, Woo, Hyeonuk, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2019

Language:

english

File:

PDF, 4.48 MB

english, 2019

41

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds

Lee, Kang-Lok, Singh, Atul K., Heo, Lim, Seok, Chaok, Roe, Jung-Hye

Journal:

Molecular Microbiology

Year:

2015

Language:

english

File:

PDF, 3.05 MB

english, 2015

42

Template-based Modeling and Ab Initio Refinement of Protein Oligomer Structures using GALAXY in CAPRI Round 30

Lee, Hasup, Baek, Minkyung, Lee, Gyu Rie, Park, Sangwoo, Seok, Chaok

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 2.03 MB

english, 2016

43

Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease

Oh, Seak Hee, Sung, Young Hoon, Kim, Inki, Sim, Chan Kyu, Lee, Jung Hoon, Baek, Minkyung, Pack, Chan-Gi, Seok, Chaok, Seo, Eul Ju, Lee, Myeong Sup, Kim, Kyung Mo

Journal:

Inflammatory Bowel Diseases

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

44

LigDockCSA: Protein–ligand docking using conformational space annealing

Woong-Hee Shin, Lim Heo, Juyong Lee, Junsu Ko, Chaok Seok, Jooyoung Lee

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 426 KB

english, 2011

45

Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies

Park, Hahnbeom, Im, Wonpil, Seok, Chaok

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

46

Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces

Seok, Chaok, Freed, Karl F., Szleifer, Igal

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 404 KB

english, 2004

47

Polymer melts and polymer solutions near patterned surfaces

Seok, Chaok, Freed, Karl F., Szleifer, Igal

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 391 KB

english, 2000

48

Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains

Kim, Jinuk, Han, Wonhee, Park, Taeyong, Kim, Eun Jin, Bang, Injin, Lee, Hyun Sik, Jeong, Yejing, Roh, Kyeonghwan, Kim, Jeesoo, Kim, Jong-Seo, Kang, Chanhee, Seok, Chaok, Han, Jin-Kwan, Choi, Hee-Jung

Journal:

Nature Communications

Year:

2020

File:

PDF, 1.54 MB

2020

49

Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller

Evangelos A. Coutsias, Chaok Seok, Ken A. Dill

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 59 KB

english, 2005

50

Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues

Lee, Sangwoo, Shin, Woong-Hee, Hong, Seongjin, Kang, Habyeong, Jung, Dawoon, Yim, Un Hyuk, Shim, Won Joon, Khim, Jong Seong, Seok, Chaok, Giesy, John P., Choi, Kyungho

Journal:

Year:

2015

Language:

english

File:

PDF, 757 KB

english, 2015

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