PUBLICATIONS

[51]

Shaima MuhammedNazaar, Jiaqi Yao, Matthew R. Necelis, Yein C. Park, Zhongtian Shen, Michael D. Bridges, Ruiqiong Guo, Nicole Swope, May S. Rhee, Miyeon Kim, Kelly H. Kim,Wayne L. Hubbell, Karen G. Fleming, Linda Columbus, Seung-gu Kang, Heedeok Hong, “The lipid bilayer strengthens the cooperative network of membrane proteins, Science Advances, 2025, https://www.science.org/doi/10.1126/sciadv.adv9568

[50]

Kwon BC, Rabinovici-Cohen S, Moturi B, R Mwaura R, K Wahome K, O Njeru O, Shinyenyi S, Wanjiru C, Remy S, Ogallo W, Guez I, Suryanarayanan P, Morrone J, Sethi S, Kang SG, Huynh T, Ng K, Mahajan D, Li H, Ninio M, Ayati S, Hexter E, Cornell W, “SPARK: Harnessing Human-Centered Workflows with Biomedical Foundation Models for Drug Discovery”, International Joint Conference on Artificial Intelligence (IJCAI-24), 2024, https://doi.org/10.24963/ijcai.2024/1015.

[49]

Weber JK, Morrone JA, Kang SG, Zhang L, Lang L, Chowell D., Krishina C, Huynh T, Parthasarathy P, Luan B, Alban TJ, Cornell WD, Chan TA, “Deep learning on molecular simulations reveals dynamical determinants of HLA-peptide complex immunogenicity”, Briefings in Bioinformatics, 2024, 25:bbad504.

[48]

Muhammednazaar S, Yao J, Guo R, Rhee SH, Kim KH, Kang SG*, Hong H*, “Lipid bilayer strengthens the cooperative network of a membrane integral enzyme”, 2023, bioRxiv, doi: https://doi.org/10.1101/2023.05.30.542905.

[47]

Kang SG*, Weber JK, Morrone JA, Zhang L, Huynh T, Cornell WD, “In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule Creation”, 2022, 62:801-16 (arXiv:2204.02513).

[46]

Zeng X, Wang F, Luo Y, Kang SG, Tang J, Lightstone FC, Fang EF, Cornell WD, Nussinov R, Cheng F, “Deep Generative Molecular Design Reshapes Drug Discovery”, Cell Reports Medicine, 2022, 3:10794. (Invited Review).

[45]

Kang SG*, Morrone JA, Weber JK, Cornell WD, “Analysis of training and seed bias in small molecules generated with a conditional graph-based variational autoencoder-Insights for practical AI-driven molecule generation”, Journal of Chemical Information and Modeling, 2022, 62:801-816 (arXiv:2107.08987).

[44]

Zhang L, Domeniconi G, Yang CC, Kang SG, Zhou R, Cong G, “CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method”, BMC Bioinformatics, 2021, 22:1-21.

[43]

Weber JK, Morrone JA, Bagchi S, Estrada Pabon JD, Kang SG, Zhang L, Cornell WD, “Simplified, interpretable graph convolutional neural networks for small molecule activity prediction”, Journal of Computer-Aided Molecular Design, 2021, https://doi.org/10.1007/s10822-021-00421-6

[42]

Guo R, Cang Z, Yao J, Kim M, Deans E, Wei G, Kang SG*, and Hong H*, “Structural cavities are critical to balancing stability and activity of a membrane-integral enzyme”, Proceedings of the National Academy of Sciences USA, 2020, 117:22146-22156.

[41]

Perez-Aguilar JM, Kang SG, Zhang L, Zhou R, “Modeling and structural characterization of the sweet taste receptor heterodimer”, ACS Chemical Neuroscience, 2019, 10:4579-92. (Featured on the cover)

[40]

Liu J†, Kang SG†, Wang P, Wang Y, Lv X, Liu Y, Wang F, Gu Z, Yang Z, Weber JK, Tao N, Qin Z, Miao Q, Chen C, Zhou R, Zhao Y, “Molecular mechanism of Gd@C82(OH)22 increasing collagen expression: Implication for encaging tumor”, Biomaterials, 2018, 152:24-36.

[39]

Chen SH†, Kang SG†, Huynh T, Zhou R, “Charging nanoparticles: Increased binding of Gd@C82(OH)22 derivatives to human MMP-9”, Nanoscale, 2018, 10:5667-77.

[38]

Meng XY†, Kang SG†, Zhou R, “Molecular mechanism of phosphoinositides' specificity for the inwardly rectifying potassium channel Kir2.2”, Chemical Science, 2018, 9:8352-62.

[37]

Bell DR†, Kang SG†, Huynh T, Zhou R, “Concentration-dependent binding of CdSe quantum dots on the SH3 domain”, Nanoscale, 2018, 10:351-8.

[36]

Joglekar AV, Liu Z, Weber JK, Ouyang Y, Jeppson JD, Noh WJ, Lamothe-Molina PA, Chen H, Kang SG, Bethune MT, Zhou R, Walker BD, Baltimore D, “T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable”, Proceedings of the National Academy of Sciences USA, 2018, 115:1877-82.

[35]

Weber JK, Kang SG, Zhou R, “Rare dissipative transitions punctuate the initiation of chemcial denaturation in proteins”, Biophysical Journal, 2018, 114:812-21.

[34]

Ling Y, Gu Z, Kang SG, Luo Z, Zhou R, “Structural damage of β-sheet protein adsorption onto MoS2 nanotube”, Journal of Physical Chemistry C, 2016, 120:6796-803.

[33]

Deng Q, Pan J, Yin X, Wang X, Zhao L, Kang SG, Jimenez-Cruz CA, Zhou R, Li J, “Toward high conductivity, selectivity and controllability of water desalination with FePc Nanopores”, Physical Chemistry Chemical Physics, 2016, 18:8140-7.

[32]

Gu Z, Yang Z, Kang SG, Yang JR, Luo Z, Zhou R, “Robust denaturation of villin headpiece by MoS2 nanosheet: Potential molecular origin of the nanotoxicity”, Scientific Reports, 2016, 6:28252.

[31]

Hölzemer A, Thobakgale CF, Jimenez-Cruz CA, Garcia-Beltran WF, Carlson JM, van Teijlingen NH, Mann JK, Jaggernath M, Kang SG, Körner C, Chung AW, Schafer JL, Evans DT, Alter G, Walker BD, Goulder PJ, Carrington M, Hartmann P, Pertel T, Zhou R, Ndung'u T, Altfeld M, “Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa”, PLos Medicine, 2015, 12:e1001900.

[30]

Pan Y, Wang L, Kang SG, Lu Y, Yang Z, Huynh T, Chen C, Zhou R, Guo M, Zhao Y, “Gd- metallofullerenol nanomaterial suppresses pancreatic cancer metastasis by inhibiting the interaction of histone deacetylase 1 and metastasis-associated protein 1”, ACS Nano, 2015, 9:6826-36.

[29]

Duan G†, Kang SG†, Tian X, Garate JA, Zhao L, Ge C, Zhou R, “Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane”, Nanoscale, 2015, 7:15214-24.

[28]

Stirnemann G, Kang SG, Zhou R, Berne BJ, “How force unfolding differs from thermal or chemical denaturation”, Proceedings of the National Academy of Sciences USA, 2014, 111:3413-8.

[27]

Kang SG, Araya-Secchi R, Wang D, Wang B, Huynh T, Zhou R, “Dual inhibitory pathways of metallofullerenol Gd@C82(OH)22 on matrix metalloproteinase-2: Molecular insight into drug-like nanomedicine”, Scientific Reports, 2014, 4:4775.

[26]

Peng Y, Swanson J, Kang SG, Zhou R, Voth G, “Hydrated excess protons can create their own water wires”, Journal of Physical Chemistry B, 2014, 119:9212-8.

[25]

Das P, Kang SG, Temple S, Belfort GE, “Interaction of Amyloid Inhibitor Proteins with Amyloid Beta Peptides: Insight from Molecular Dynamics Simulations”, PLos One, 2014, 9:e113041.

[24]

Gao J, Wang L, Kang SG, Zhao L, Ji M, Chen C, Li J, Zhao Y, Zhou R, “Size-dependent impact of CNT on dynamics properties of calmodulin”, Nanoscale, 2014, 6:12828-37.

[23]

Yang X†, Kang SG†, Zhou R, “Nanomedicine: de novo design of nanodrugs”, Nanoscale, 2014, 6:663-77.

[22]

Gao Y, Dai X, Kang SG, Jimenez-Cruz CA, Xin M, Meng Y, Han J, Wang Z, Zhou R, “Structural and electronic properties of uranium-encapsulated Au14 cage”, Scientific Reports, 2014, 4:5862.

[21]

Jimenez-Cruz C, Kang SG, Zhou R, “Large-scale molecular simulations for nanotoxicity”, WIREs Systems Biology and Medicine, 2014, 6:329-43.

[20]

Gao Y, Zhou B, Kang SG, Xin M, Yang P, Dai X, Wang Z, Zhou R, “Effect of ligands on characteristics of (CdSe)13 quantum dot”, RSC Advances, 2014, 4:27146-51.

[19]

Araya-Secchi R†, Perez-Acle T†, Kang SG, Huynh T, Bernardin A, Escalona Y, Garate JA, Martinez AD, Garcia IE, Saez JC, Zhou R, “Characterization of a novel water pocket inside the human Cx26 hemi-channel structure”, Biophysical Journal, 2014, 107:599-612.

[18]

Kang SG, Das P, McGrane SJ, Martin AJ, Huynh T, Royyuru AK, Taylor AJ, Jones PG, Zhou R, “Molecular recognition of metabotropic glutamate receptor type 1 (mGluR1): Synergistic: understanding with free energy perturbation and linear response modeling”, Journal of Physical Chemistry B, 2014, 118:6393-404.

[17]

Xia Z†, Chen H†, Kang SG, Huynh T, Fang J, Lamothe P, Walker B, Zhou R, “The complex and specific pMHC interactions with diverse HIV-1 TCR clonotypes reveal a structural basis for alterations in CTL function”, Scientific Reports, 2014, 4:4087.

[16]

Dai B†, Kang SG†, Huynh T, Lei H, Castelli M, Hu J, Zhang Y, Zhou R, “Salts drive controllable multi-layered upright assembly of amyloid-like peptides at mica/water interface”, Proceedings of the National Academy of Sciences USA, 2013, 110:8543-8.

[15]

Yin X†, Zhao L†, Kang SG, Pan J, Song Y, Zhang M, Xing G, Wang F, Li J, Zhou R, Zhao Y, “Impact of fullerene derivatives on regulating the structure and assembly of collagen molecules”, Nanoscale, 2013, 5:7341-8.

[14]

Kang SG, Huynh T, Zhou R, “Metallofullerenol Gd@C82(OH)22 distracts the proline-rich motif from putative binding on the SH3 domain”, Nanoscale, 2013, 5:2703-12.

[13]

Kang SG, Huynh T, Xia Z, Zhang Y, Fang H, Wei G, Zhou R, “Hydrophobic interaction drives suface-assisted epitaxial assembly of amyloid-like peptides”, Journal of the American Chemical Society, 2013, 135:3150-7.

[12]

Kang SG, Huynh T, Zhou R, “Non-destructive inhibition of metallofullenol Gd@C82(OH)22 on WW domain: Implication on signal transduction pathway”, Scientific Reports, 2012, 2:957.

[11]

Kang SG, Li H, Huynh T, Zhang F, Xia Z, Zhang Y, Zhou R, “Molecular mechanism of surface-assisted epitaxial self-assembly of amyloid-like peptides”, ACS Nano, 2012, 6:9276-82.

[10]

Zuo G, Kang SG, Xiu P, Zhao Y, Zhou R, “Interaction between proteins and carbon-based nanoparticles: Exploring the origin of nanotoxicity at the molecular level”, Small, 2012, DOI:10.1002/smll.201201381.

[9]

Kang SG, Zhou G, Yang P, Liu Y, Sun B, Huynh T, Meng H, Zhao L, Xing G, Chen C, Zhao Y, Zhou R, “Molecular mechanism of pancreatic tumor metastasis inhibition by Gd@C82(OH)22 and its implication for de novo design of nanomedicine”, Proceedings of the National Academy of Sciences USA, 2012, 109:15431-6. (Featured in PNAS Highlight, MIT-Technology Review, Nature-SciBX, PNNL News and IBM Research)

[8]

Lanci CJ†, MacDermaid CM†, Kang SG, Acharya R, North B, Yang X, Qiu XJ, DeGrado WF, Saven JG, “Computation design of a protein crystal”, Proceedings of the National Academy of Sciences USA, 2012, 109:7304-9. (Featured in C&En Chemical and Engineering News)

[7]

Xia Z, Huynh T, Kang SG, Zhou R, “Free energy simulation reveal that both hydrophobic and polar interactions are important for influenza hemagglutinin antibody binding”, Biophysical Journal, 2012, 102:1453-61.

[6]

Park SJ, Kang SG, Saven JG, Park SJ, "Highly tunable photoluminescent properties of amphiphilic conjugated block copolymers", Journal of the American Chemical Society, 2010, 132:9331-33.

[5]

Kang SG, "Probabilistic computational protein design: Advances in methodology and the incorporation of non-biological molecular component", Doctoral Dissertation Thesis, University of Pennsylvania, 2009.

[4]

Tang J†, Kang SG†, Saven JG, Gai F, "Characterization of the cofactor-induced folding mechanism of a zinc-binding peptide using computationally designed mutants", Journal of Molecular Biology, 2009, 389:90-102.

[3]

Butts CA, Swift J, Kang SG, Constanzo LD, Christianson DW, Saven JG, Dmochowski IJ, "Directing noble metal ion chemistry within a designed ferritin protein", Biochemistry, 2008, 47:12729-39.

[2]

Kang SG, Saven JG, "Computational protein design: structure, function and combinatorial diversity", Current Opinion in Chemical Biology, 2007, 11:329-34.

[1]

Kang SG, Chae WS, Kim YR, Jung JS, Lee SH, "Electronic energy dynamics of photoexcited ternary Zintl phase LiSbTe2 and the distance estimation between trap sites", Chemical Physics, 2000, 256:295-305.