Refereed Journals

  1. Hyuntae Na*, Guang Song, "Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens," J. Chem. Theory Comput. 2023 Oct 24; 9(20):7307-7323. doi: 10.1021/acs.jctc.3c00700
  2. Hyuntae Na, Guang Song*, "Towards a free energy-based elastic network model and its application to the SARS-COV2 binding to ACE2," Physical Biology. 2023 May 30; 20(4):046005. doi: 10.1088/1478-3975/acd6cd
  3. In Jung Kim, Hyuntae Na*, "An Efficient Algorithm Calculating Common Solvent Accessible Volume," PLoS ONE. 2022 Mar 21; 17(3):e0265614. doi: 10.1371/journal.pone.0265614
  4. Hyuntae Na, Konrad Hinsen, Guang Song*, "The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors," Proteins. 2021 Nov; 89(11):1442-1457. doi: 10.1002/prot.26165
  5. Anshuman Bose Majumdar, Injung Kim, Hyuntae Na*, "Effect of solvent on protein structure and dynamics," Physical Biology. 2020 Apr 8; 17(3):036006. doi: 10.1088/1478-3975/ab74b3
  6. Hyuntae Na, Daniel ben-Avraham, Monique M. Tirion*, "Slow Normal Modes of Proteins are Accurately Reproduced across Different Platforms," Physical Biology. 2018 Nov 7; 16(1):016003. doi: 10.1088/1478-3975/aae333
  7. Hyuntae Na*, Guang Song, "All-atom normal mode dynamics of HIV-1 capsid," PLoS Comput. Biol. 2018 Sep 18; 14(9):e1006456. doi: 10.1371/journal.pcbi.1006456
  8. Hyuntae Na, Guang Song*, "Fast Normal Mode Computations of Capsid Dynamics Inspired by Resonance," Physical Biology. 2018 Apr 30; 15(4):046003. doi: 10.1088/1478-3975/aab813
  9. Hyuntae Na, Guang Song*, "Predicting the functional motions of p97 using symmetric normal modes," Proteins. 2016 Dec;84(12)1823-1835. doi:10.1002/prot.25164
    (Cover Image, Volume 84, Issue 12, doi:10.1002/prot.25195)
  10. Hyuntae Na, Guang Song*, "The Effective Degeneracy of Protein Normal Modes," Phys Biol. 2016 May 12; 13(3):036002. doi: 10.1088/1478-3975/13/3/036002
  11. Hyuntae Na, Guang Song*, Daniel ben-Avraham, "Universality of vibrational spectra of globular proteins," Phys Biol. 2016 Feb 23;13(1):016008. doi: 10.1088/1478-3975/13/1/016008. (link)
  12. Hyuntae Na, Robert L. Jernigan, Guang Song*, "Bridging between NMA and Elastic Network Models: Preserving All-atom Accuracy in Coarse-grained Models," PLoS Comput. Biol. 2015 Oct 16;11(10):e1004542. doi: 10.1371/journal.pcbi.1004542 (link)
  13. Hyuntae Na, Guang Song*, "The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors," Proteins. 2015 Jul;83(7):1273-1283. doi: 10.1002/prot.24819 (link)
  14. Hyuntae Na, Guang Song*, "Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants," Proteins. 2015 Apr;83(4):757-70. doi: 10.1002/prot.24770 (link)
  15. Hyuntae Na, Guang Song*, "Conventional NMA as a better standard for evaluating elastic network models," Proteins. 2015 Feb;83(2):259-67. doi: 10.1002/prot.24735 (link)
  16. Hyuntae Na, Guang Song*, "Bridging between normal mode analysis and elastic network models," Proteins. 2014 Sep;82(9):2157-68. doi: 10.1002/prot.24571 (link)
  17. Hyuntae Na, Guang Song*, "A natural unification of GNM and ANM and the role of inter-residue forces," Physical Biology. Vol. 11. No. 3, 2014. (link)
  18. Hyuntae Na, Seung-Yub Lee, Ersan Üstündag, Sarah L. Ross, Halil Ceylan, and Kasthurirangan Gopalakrishnan*, "Development of a Neural Network Simulator for Studying the Constitutive Behavior of Structural Composite Materials," ISRN Materials Science, vol. 2013, Article ID 147086, 10 pages, 2013. doi:10.1155/2013/147086.(link)
  19. Jong Ryul Kim, Hyun Tae Na, Young Shik Moon*, "A Robust Algorithm for Tracking Non-rigid Objects Using Deformed Template and Level-Set Theory", Journal of IEEK, 2003, 5. (link)

Book Chapter

  1. Hyuntae Na, Tu-Liang Lin, and Guang Song. Generalized Spring Tensor Models for Protein Fluctuation Dynamics and Conformation Changes. In: Protein Conformational Dynamics (Ed. Ke-Li Han, Xin Zhang, Ming-jun Yang), Advances in Experimental Medicine and Biology, Vol. 805, pages 107-135, Springer, 2014.
    http://www.ncbi.nlm.nih.gov/pubmed/24446359

Theses

  1. Hyuntae Na, "Normal mode computations and applications" (2016). Graduate Theses and Dissertations. Paper 15071.
    http://lib.dr.iastate.edu/etd/15071
  2. Hyuntae Na, "An online algorithm for matching noisy space curves with statistical error analysis" (2011). Graduate Theses and Dissertations. Paper 12239.
    http://lib.dr.iastate.edu/etd/12239
  3. Hyuntae Na, "Object Tracking Algorithm using Deformed Template and Level-Set Theory" (2002). Hanyang University (link)

Refereed Conferences

  1. Hyuntae Na, Guang Song, "An Efficient Method for Quantitative Delineation of How Protein Breathing Motions Open Ligand Migration Channels," Workshop on Robotics Methods for Structural and Dynamic Modeling of Molecular Systems, 7 pages, July 2014.
    doi: 10.1016/j.bpj.2018.11.1873
  2. Hyuntae Na, Guang Song, "Ellipsoid-weighted Protein Conformation Alignment," International Symposium on Bioinformatics Research and Applications, Lecture Notes in Computer Science, Vol. 7875, pages 273-285, May 2013.
    http://link.springer.com/chapter/10.1007%2F978-3-642-38036-5_27
  3. Jong Ryul Kim, Hyun Tae Na, Young Shik Moon, "A Robust Algorithm for Tracking Non-rigid Objects," International Technical Conference on Circuits/Systems, Computers and Communications, pages 142-145, July 2002.
    http://www.dbpia.co.kr/Article/NODE01750337
  4. Jong Ryul Kim, Hyun Tae Na, Young Shik Moon, "Object Tracking using Parametric Motion Model and Edge Information," Workshop of Special Interest Group on Computer Vision & Pattern Recognition, November 2002.
  5. Hyun Tae Na, Young Shik Moon, "Object tracking using Template Deformation and Level-Set Theory," Workshop of Special Interest Group on Computer Vision and Pattern Recognition, November 2001.
  6. Jong Ryul Kim, Hyun Tae Na, Jung-Sun Kim, Young Shik Moon, "Performance Evaluation of Parallel BMA on Networked Cluster of Workstations," Workshop of Korean Institute of Information Scientists and Engineers, Vol. 26, No. 2, pages 753-755, October 1999.
    http://www.dbpia.co.kr/Article/NODE00608448

Posters

  1. Anshuman Bose Majumdar, Injung Kim, Hyuntae Na, "The Contribution of a Solvent on Protein Dynamics," Biophysical Journal, Baltimore, Maryland, March 2-6, 2019.
    https://doi.org/10.1016/j.bpj.2018.11.1873
  2. Hyuntae Na, Guang Song, "BOSE: the Functional Low Frequency Modes of Very Large Systems with Atomic Accuracy using Blocks of Selected Elasticity, and its application to HIV-1 capsid," Protein Society 32nd Annual Symposium, Boston, Massachusetts, July 9-12, 2018.
  3. Hyuntae Na, Guang Song, Daniel ben-Avraham, "Universality of Vibrational Spectra of Globular Proteins," Biophysical Journal. 2016 Feb 16; 110(3); p53a.
    http://www.cell.com/biophysj/fulltext/S0006-3495(15)01535-0
  4. Hyuntae Na, Guang Song, "The Degeneracy of Protein Normal Modes," Biophysical Journal. 2016 Feb 16; 110(3); p53a-54a.
    http://www.cell.com/biophysj/fulltext/S0006-3495(15)01536-2

Professional Services

  • Program committee, Computational Structural Bioinformatics Workshop 2020 in conjunction with ACM-BCB, Sept. 21-24, Atlanta GA
  • Chair of session 3, Creativity in Drug Discovery. Protein Society 32nd Annual Symposium, Boston, Massachusetts, July 9-12, 2018. (appointed)
  • Poster judge, Protein Society 32nd Annual Symposium. Boston, Massachusetts, July 9-12, 2018.