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1

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

Elmar Krieger, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Srivatsan Raman, James Thompson, Mike Tyka, David Baker, Kevin Karplus

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 173 KB

english, 2009

2

Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing

Jinwoo Lee, Keehyoung Joo, Seung-Yeon Kim, Jooyoung Lee

Journal:

Journal of Computational Chemistry

Année:

2008

Langue:

english

Fichier:

PDF, 314 KB

english, 2008

3

Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

Joung, InSuk, Kim, Jong Yun, Gross, Steven P., Joo, Keehyoung, Lee, Jooyoung

Journal:

Computer Physics Communications

Année:

2018

Langue:

english

Fichier:

PDF, 560 KB

english, 2018

4

Necessary and sufficient conditions for the asymmetric synthesis of chiral amines using ω-aminotransferases

Joo-Hyun Seo, Dohyun Kyung, Keehyoung Joo, Jooyoung Lee, Byung-Gee Kim

Journal:

Biotechnology and Bioengineering

Année:

2011

Langue:

english

Fichier:

PDF, 439 KB

english, 2011

5

Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening

Joo-Hyun Seo, Gang-Seong Lee, Juhan Kim, Byung-Kwan Cho, Keehyoung Joo, Jooyoung Lee, Byung-Gee Kim

Journal:

Enzyme and Microbial Technology

Année:

2009

Langue:

english

Fichier:

PDF, 611 KB

english, 2009

6

Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing

Julian Lee, Seung-Yeon Kim, Keehyoung Joo, Ilsoo Kim, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2004

Langue:

english

Fichier:

PDF, 1.32 MB

english, 2004

7

High accuracy template based modeling by global optimization

Keehyoung Joo, Jinwoo Lee, Sunjoong Lee, Joo-Hyun Seo, Sung Jong Lee, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 565 KB

english, 2007

8

Assessment of predictions submitted for the CASP7 domain prediction category

Michael Tress, Jianlin Cheng, Pierre Baldi, Keehyoung Joo, Jinwoo Lee, Joo-Hyun Seo, Jooyoung Lee, David Baker, Dylan Chivian, David Kim, Iakes Ezkurdia

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2007

9

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing

Keehyoung Joo, Jinwoo Lee, Joo-Hyun Seo, Kyoungrim Lee, Byung-Gee Kim, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 965 KB

english, 2009

10

Protein-binding site prediction based on three-dimensional protein modeling

Mina Oh, Keehyoung Joo, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 338 KB

english, 2009

11

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

Année:

2011

Langue:

english

Fichier:

PDF, 950 KB

english, 2011

12

Design and efficient production of bovine enterokinase light chain with higher specificity inE. coli

Haarin Chun, Keehyoung Joo, Jooyoung Lee, Hang-Cheol Shin

Journal:

Biotechnology Letters

Année:

2011

Langue:

english

Fichier:

PDF, 269 KB

english, 2011

13

Sann: Solvent accessibility prediction of proteins by nearest neighbor method

Keehyoung Joo, Sung Jong Lee, Jooyoung Lee

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

14

Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions

Jae-Sung Woo, Jae-Hong Lim, Ho-Chul Shin, Min-Kang Suh, Bonsu Ku, Kwang-Hoon Lee, Keehyoung Joo, Howard Robinson, Jooyoung Lee, Sam-Yong Park, Nam-Chul Ha, Byung-Ha Oh

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 4.55 MB

english, 2009

15

Multiple Sequence Alignment by Conformational Space Annealing

Joo, Keehyoung, Lee, Jinwoo, Kim, Ilsoo, Lee, Sung Jong, Lee, Jooyoung

Journal:

Biophysical Journal

Année:

2008

Langue:

english

Fichier:

PDF, 169 KB

english, 2008

16

WESTMINSTER HOSPITAL.

Lee, Jooyoung, Lee, Jinhyuk, Joo, Keehyoung, Lee, Jinwoo

Journal:

Année:

1831

Langue:

english

Fichier:

PDF, 211 KB

english, 1831

17

NMR Structure Determination by Conformational Space Annealing

Lee, Jooyoung, Lee, Jinhyuk, Joo, Keehyoung, Lee, Jinwoo

Journal:

Biophysical Journal

Année:

2011

Langue:

english

Fichier:

PDF, 37 KB

english, 2011

18

Biological oceanography

Lee, Jooyoung, Lee, Jinhyuk, Joo, Keehyoung, Lee, Jinwoo

Journal:

Deep Sea Research Part B. Oceanographic Literature Review

Année:

1980

Langue:

english

Fichier:

PDF, 2.01 MB

english, 1980

19

Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm

Seo, Joo-Hyun, Park, Jihyang, Kim, Eun-Mi, Kim, Juhan, Joo, Keehyoung, Lee, Jooyoung, Kim, Byung-Gee

Journal:

Computational Biology and Chemistry

Année:

2014

Langue:

english

Fichier:

PDF, 575 KB

english, 2014

20

Protein Structure Determination by Molecular Replacement using High-Accuracy Protein Structure Modeling

Joo, Keehyoung, Kim, Mi-Sun, Han, Jeong Hae, Shin, Dong Hae, Lee, Jooyoung

Journal:

Biophysical Journal

Année:

2010

Langue:

english

Fichier:

PDF, 40 KB

english, 2010

21

Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method

Okur, Asim, Miller, Benjamin T., Joo, Keehyoung, Lee, Jooyoung, Brooks, Bernard R.

Journal:

Journal of Chemical Theory and Computation

Année:

2013

Langue:

english

Fichier:

PDF, 2.71 MB

english, 2013

22

Structural basis of intersubunit recognition in elongin BC–cullin 5–SOCS box ubiquitin–protein ligase complexes

Kim, Young Kwan, Kwak, Mi-Jeong, Ku, Bonsu, Suh, Hye-Young, Joo, Keehyoung, Lee, Jooyoung, Jung, Jae U., Oh, Byung-Ha

Journal:

Acta Crystallographica Section D Biological Crystallography

Année:

2013

Langue:

english

Fichier:

PDF, 2.38 MB

english, 2013

23

Protein structure modeling for CASP10 by multiple layers of global optimization

Joo, Keehyoung, Lee, Juyong, Sim, Sangjin, Lee, Sun Young, Lee, Kiho, Heo, Seungryong, Lee, In-Ho, Lee, Sung Jong, Lee, Jooyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 684 KB

english, 2014

24

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

Lee, Juyong, Lee, Kiho, Joung, InSuk, Joo, Keehyoung, Brooks, Bernard R, Lee, Jooyoung

Journal:

BMC Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 3.03 MB

english, 2015

25

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Krupa, Paweł, Mozolewska, Magdalena A., Joo, Keehyoung, Lee, Jooyoung, Czaplewski, Cezary, Liwo, Adam

Journal:

Journal of Chemical Information and Modeling

Année:

2015

Langue:

english

Fichier:

PDF, 3.90 MB

english, 2015

26

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

Lee, Juyong, Joo, Keehyoung, Brooks, Bernard R., Lee, Jooyoung

Journal:

Journal of Chemical Theory and Computation

Année:

2015

Langue:

english

Fichier:

PDF, 4.99 MB

english, 2015

27

Protein Structure Determination by Conformational Space Annealing using NMR Geometric Restraints

Lee, Jooyoung, Joo, Keehyoung, Joung, InSuk, Lee, Jinhyuk, Lee, Jinwoo, Lee, Weontae, Brooks, Bernard, Lee, Sung Jong

Journal:

Biophysical Journal

Année:

2016

Langue:

english

Fichier:

PDF, 42 KB

english, 2016

28

Template based protein structure modeling by global optimization in CASP11

Joo, Keehyoung, Joung, InSuk, Lee, Sun Young, Kim, Jong Yun, Cheng, Qianyi, Manavalan, Balachandran, Joung, Jong Young, Heo, Seungryong, Lee, Juyong, Nam, Mikyung, Lee, In-Ho, Lee, Sung Jong, Lee, Joo

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 882 KB

english, 2015

29

Contact assisted protein structure modeling by global optimization in CASP11

Joo, Keehyoung, Joung, InSuk, Cheng, Qianyi, Lee, Sung Jong, Lee, Jooyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 916 KB

english, 2015

30

Template Free Modeling by LEE and LEER in CASP11

Joung, InSuk, Lee, Sun Young, Cheng, Qianyi, Kim, Jong Yun, Joo, Keehyoung, Lee, Sung Jong, Lee, Jooyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 932 KB

english, 2015

31

Protein structure determination by conformational space annealing using NMR geometric restraints

Joo, Keehyoung, Joung, InSuk, Lee, Jinhyuk, Lee, Jinwoo, Lee, Weontae, Brooks, Bernard, Lee, Sung Jong, Lee, Jooyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 354 KB

english, 2015

32

Use of Restraints from Consensus Fragments of Multiple Server Models to Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Mozolewska, Magdalena Anna, Krupa, Pawel, Zaborowski, Bartlomiej, Liwo, Adam, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary

Journal:

Journal of Chemical Information and Modeling

Année:

2016

Langue:

english

Fichier:

PDF, 1.61 MB

english, 2016

33

Folding Mechanisms of Small Proteins GB1 and LB1

Cheng, Qianyi, Joung, Insuk, Joo, Keehyoung, Kuwajima, Kunihiro, Lee, Jooyoung

Journal:

Biophysical Journal

Année:

2017

Langue:

english

Fichier:

PDF, 56 KB

english, 2017

34

Protein Loop Structure Prediction Using Conformational Space Annealing

Heo, Seungryong, Lee, Juyong, Joo, Keehyoung, Shin, Hang-Cheol, Lee, Jooyoung

Journal:

Journal of Chemical Information and Modeling

Année:

2017

Langue:

english

Fichier:

PDF, 5.10 MB

english, 2017

35

Architecture of the type IV coupling protein complex of Legionella pneumophila

Kwak, Mi-Jeong, Kim, J. Dongun, Kim, Hyunmin, Kim, Cheolhee, Bowman, James W., Kim, Seonghoon, Joo, Keehyoung, Lee, Jooyoung, Jin, Kyeong Sik, Kim, Yeon-Gil, Lee, Nam Ki, Jung, Jae U., Oh, Byung-Ha

Journal:

Nature Microbiology

Année:

2017

Langue:

english

Fichier:

PDF, 7.90 MB

english, 2017

36

Methods for estimation of model accuracy in CASP12

Elofsson, Arne, Joo, Keehyoung, Keasar, Chen, Lee, Jooyoung, Maghrabi, Ali H. A., Manavalan, Balachandran, McGuffin, Liam J., Ménendez Hurtado, David, Mirabello, Claudio, Pilstål, Robert, Sidi, Tomer,

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.70 MB

english, 2017

37

Protein Structure Modeling and Refinement by Global Optimization in CASP12

Hong, Seung Hwan, Joung, InSuk, Flores-Canales, Jose C., Manavalan, Balachandran, Cheng, Qianyi, Heo, Seungryong, Kim, Jong Yun, Lee, Sun Young, Nam, Mikyung, Joo, Keehyoung, Lee, In-Ho, Lee, Sung Jon

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2017

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2017

38

An artificially constructed dimer through deformation of a short zinc-binding loop

Park, Jimin, Kim, Mi-Sun, Joo, Keehyoung, Lee, Jooyoung, Shin, Dong Hae

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Année:

2018

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2018

39

Data-Assisted Protein Structure Modeling by Global Optimization in CASP12

Joo, Keehyoung, Heo, Seungryong, Joung, InSuk, Hong, Seung Hwan, Lee, Sung Jong, Lee, Jooyoung

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2018

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2018

40

Morphological Evaluation of Meta-stable Oligomers of α-Synuclein with Small-Angle Neutron Scattering

Bhak, Ghibom, Lee, Soonkoo, Kim, Tae-Hwan, Lee, Ji-Hye, Yang, Jee Eun, Joo, Keehyoung, Lee, Jooyoung, Char, Kookheon, Paik, Seung R.

Journal:

Scientific Reports

Année:

2018

Langue:

english

Fichier:

PDF, 2.52 MB

english, 2018

41

ConDo: Protein domain boundary prediction using coevolutionary information

Hong, Seung Hwan, Joo, Keehyoung, Lee, Jooyoung, Valencia, Alfonso

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.58 MB

english, 2018

42

A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction

Han, Jeongmin, Kim, Iktae, Park, Jae-Hyun, Yun, Ji-Hye, Joo, Keehyoung, Kim, Taehee, Park, Gye-Young, Ryu, Kyoung-Seok, Ko, Yoon-Joo, Mizutani, Kenji, Park, Sam-Young, Seong, Rho Hyun, Lee, Jooyoung,

Journal:

International Journal of Molecular Sciences

Année:

2020

Fichier:

PDF, 5.77 MB

2020