New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. - Jooyoung Lee 002; Harold A. Scheraga; Shelly Rackovsky (J. Comput. Chem., 1997)

Surmounting the Multiple-Minima Problem in Protein Folding. - Harold A. Scheraga; Jooyoung Lee 002; Jaroslaw Pillardy; Yuan-Jie Ye; Adam Liwo; Daniel R. Ripoll (J. Glob. Optim., 1999)

UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. - Adam Liwo; Jaroslaw Pillardy; Cezary Czaplewski; Jooyoung Lee 002; Daniel R. Ripoll; Malgorzata Groth; Sylwia Rodziewicz-Motowidlo; Rajmund Kazmierkiewicz; Ryszard J. Wawak; Stanislaw Oldziej; Harold A. Scheraga (RECOMB, 2000)

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. - Harold A. Scheraga; Jaroslaw Pillardy; Adam Liwo; Jooyoung Lee 002; Cezary Czaplewski; Daniel R. Ripoll; William J. Wedemeyer; Yelena A. Arnautova (J. Comput. Chem., 2002)

An efficient molecular docking using conformational space annealing. - Kyoungrim Lee; Cezary Czaplewski; Seung-Yeon Kim; Jooyoung Lee 002 (J. Comput. Chem., 2005)

Application of the multiensemble sampling to the equilibrium folding of proteins. - Hyeon S. Son; Seung-Yeon Kim; Jooyoung Lee 002; Kyu-Kwang Han (Bioinform., 2006)

Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing. - Jinwoo Lee; Keehyoung Joo; Seung-Yeon Kim; Jooyoung Lee 002 (J. Comput. Chem., 2008)

Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure. - In-Ho Lee 004; Seung-Yeon Kim; Jooyoung Lee 002 (J. Comput. Chem., 2010)

LigDockCSA: Protein-ligand docking using conformational space annealing. - Woong-Hee Shin; Lim Heo; Juyong Lee; Junsu Ko; Chaok Seok; Jooyoung Lee 002 (J. Comput. Chem., 2011)

Mod-CSA: Modularity optimization by conformational space annealing - Juyong Lee; Steven P. Gross; Jooyoung Lee 002 (CoRR, 2012)

Extraction of hidden information by efficient community detection in networks - Juyong Lee; Steven P. Gross; Jooyoung Lee 002 (CoRR, 2012)

Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. - Joo-Hyun Seo; Jihyang Park; Eun-Mi Kim; Juhan Kim; Keehyoung Joo; Jooyoung Lee 002; Byung-Gee Kim (Comput. Biol. Chem., 2014)

Structure-based protein folding type classification and folding rate prediction. - Balachandran Manavalan; Kunihiro Kuwajima; InSuk Joung; Jooyoung Lee 002 (BIBM, 2015)

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. - Juyong Lee; Kiho Lee; InSuk Joung; Keehyoung Joo; Bernard R. Brooks; Jooyoung Lee 002 (BMC Bioinform., 2015)

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. - Pawel Krupa; Magdalena A. Mozolewska; Keehyoung Joo; Jooyoung Lee 002; Cezary Czaplewski; Adam Liwo (J. Chem. Inf. Model., 2015)

Link community detection through global optimization and the inverse resolution limit of partition density. - Juyong Lee; Zhong-Yuan Zhang; Jooyoung Lee 002; Bernard R. Brooks; Yong-Yeol Ahn (CoRR, 2016)

Ab initio materials design using conformational space annealing and its application to searching for direct band gap silicon crystals. - In-Ho Lee 004; Young Jun Oh; Sunghyun Kim 002; Jooyoung Lee 002; Kee Joo Chang (Comput. Phys. Commun., 2016)

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. - Magdalena A. Mozolewska; Pawel Krupa; Bartlomiej Zaborowski; Adam Liwo; Jooyoung Lee 002; Keehyoung Joo; Cezary Czaplewski (J. Chem. Inf. Model., 2016)

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. - Agnieszka S. Karczynska; Cezary Czaplewski; Pawel Krupa; Magdalena A. Mozolewska; Keehyoung Joo; Jooyoung Lee 002; Adam Liwo (J. Comput. Chem., 2017)

Protein Loop Structure Prediction Using Conformational Space Annealing. - Seungryong Heo; Juyong Lee; Keehyoung Joo; Hang-Cheol Shin; Jooyoung Lee 002 (J. Chem. Inf. Model., 2017)

Conformational Space Annealing explained: A general optimization algorithm, with diverse applications. - InSuk Joung; Jong Yun Kim; Steven P. Gross; Keehyoung Joo; Jooyoung Lee 002 (Comput. Phys. Commun., 2018)

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. - Agnieszka S. Karczynska; Karolina Zieba; Urszula Uciechowska; Magdalena A. Mozolewska; Pawel Krupa; Emilia A. Lubecka; Agnieszka G. Lipska; Celina Sikorska; Sergey A. Samsonov; Adam K. Sieradzan; Artur Gieldon; Adam Liwo; et al. (J. Chem. Inf. Model., 2020)

Application of conformational space annealing to the protein structure modeling using cryo-EM maps. - Jimin Park; InSuk Joung; Keehyoung Joo; Jooyoung Lee 002 (J. Comput. Chem., 2023)