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Chia-en Chang, Ph.D. - Publications

Affiliations: 
2003 University of Maryland, College Park, College Park, MD 
Area:
Physical Chemistry, General Biophysics, Medical Biophysics, Pharmaceutical Chemistry
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Miao Y, Chang CA, Zhu W, McCammon JA. Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning. Frontiers in Molecular Biosciences. 10: 1139471. PMID 36733435 DOI: 10.3389/fmolb.2023.1139471  0.436
2022 Chen W, He H, Wang J, Wang J, Chang CA. Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics. Physical Chemistry Chemical Physics : Pccp. PMID 36562309 DOI: 10.1039/d2cp04584b  0.334
2022 Ruzmetov T, Montes R, Sun J, Chen SH, Tang Z, Chang CA. Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes. The Journal of Physical Chemistry. A. PMID 36346951 DOI: 10.1021/acs.jpca.2c05499  0.438
2022 Sun J, Raymundo MAV, Chang CA. Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison. Life (Basel, Switzerland). 12. PMID 35054509 DOI: 10.3390/life12010116  0.401
2021 Kaushik S, Chang CA. Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association. Frontiers in Molecular Biosciences. 8: 659687. PMID 34041265 DOI: 10.3389/fmolb.2021.659687  0.309
2020 Bosken YK, Cholko T, Lou YC, Wu KP, Chang CA. Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease. Frontiers in Molecular Biosciences. 7: 174. PMID 32850963 DOI: 10.3389/Fmolb.2020.00174  0.353
2020 Tang Z, Chen SH, Chang CA. Transient states and barriers from molecular simulations and milestoning theory: kinetics in ligand-protein recognition and compound design. Journal of Chemical Theory and Computation. PMID 32031801 DOI: 10.1021/acs.jctc.9b01153  0.409
2019 You W, Tang Z, Chang CA. Potential mean force from umbrella sampling simulations: what can we learn and what is missed? Journal of Chemical Theory and Computation. PMID 30811931 DOI: 10.1021/acs.jctc.8b01142  0.359
2018 Cholko T, Chen W, Tang Z, Chang CA. A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery. Journal of Computer-Aided Molecular Design. PMID 29737445 DOI: 10.1007/s10822-018-0120-3  0.417
2018 You W, Chang CA. Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. Journal of Chemical Information and Modeling. PMID 29620886 DOI: 10.1021/acs.jcim.7b00640  0.346
2018 Miao Y, Huang YM, Walker RC, McCammon JA, Chang CA. Ligand Binding Pathways and Conformational Transitions of the HIV Protease. Biochemistry. PMID 29394043 DOI: 10.1021/Acs.Biochem.7B01248  0.542
2017 Tang Z, Chang CA. Systematic Dissociation Pathway Searches Guided by Principal Component Modes. Journal of Chemical Theory and Computation. PMID 28418661 DOI: 10.1021/acs.jctc.6b01204  0.335
2017 Huang YM, Raymundo MA, Chen W, Chang CA. Mechanism of the association pathways for a pair of fast and slow binding ligands of HIV-1 protease. Biochemistry. PMID 28060481 DOI: 10.1021/acs.biochem.6b01112  0.403
2017 Tang Z, Roberts CC, Chang CA. Understanding ligand-receptor non-covalent binding kinetics using molecular modeling. Frontiers in Bioscience (Landmark Edition). 22: 960-981. PMID 27814657  0.327
2016 You W, Huang YM, Kizhake S, Natarajan A, Chang CA. Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. Plos Computational Biology. 12: e1005057. PMID 27560145 DOI: 10.1371/Journal.Pcbi.1005057  0.351
2014 Huang YM, Kang M, Chang CE. Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. Journal of Molecular Recognition : Jmr. 27: 537-48. PMID 25042708 DOI: 10.1002/Jmr.2377  0.32
2014 Huang YM, Chang CE. Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain. Plos One. 9: e98291. PMID 24870410 DOI: 10.1371/journal.pone.0098291  0.307
2013 Roberts CC, Chang CE. Ligand Binding Pathway Elucidation for Cryptophane Host-Guest Complexes. Journal of Chemical Theory and Computation. 9: 2010-9. PMID 26583550 DOI: 10.1021/ct301023m  0.399
2012 Huang YM, Kang M, Chang CE. Mechanistic insights into phosphopeptide--BRCT domain association: preorganization, flexibility, and phosphate recognition. The Journal of Physical Chemistry. B. 116: 10247-58. PMID 22857521 DOI: 10.1021/Jp305028D  0.314
2012 Huang YM, Chen W, Potter MJ, Chang CE. Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes. Biophysical Journal. 103: 342-51. PMID 22853912 DOI: 10.1016/j.bpj.2012.05.046  0.401
2011 Kang M, Roberts C, Cheng Y, Chang CE. Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease. Journal of Chemical Theory and Computation. 7: 3438-46. PMID 26598172 DOI: 10.1021/Ct2004885  0.38
2010 Fatmi MQ, Chang CE. The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase. Plos Computational Biology. 6: e1000994. PMID 21085641 DOI: 10.1371/journal.pcbi.1000994  0.31
2009 Fatmi MQ, Ai R, Chang CEA. Synergistic regulation and ligand-induced conformational changes of tryptophan synthase Biochemistry. 48: 9921-9931. PMID 19764814 DOI: 10.1021/bi901358j  0.336
2008 Cheng Y, Chang CE, Yu Z, Zhang Y, Sun M, Leyh TS, Holst MJ, McCammon JA. Diffusional channeling in the sulfate-activating complex: combined continuum modeling and coarse-grained brownian dynamics studies. Biophysical Journal. 95: 4659-67. PMID 18689458 DOI: 10.1529/Biophysj.108.140038  0.351
2008 Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 105: 7456-61. PMID 18495919 DOI: 10.1073/Pnas.0800452105  0.469
2008 Gorfe AA, Chang CE, Ivanov I, McCammon JA. Dynamics of the acetylcholinesterase tetramer. Biophysical Journal. 94: 1144-54. PMID 17921202 DOI: 10.1529/Biophysj.107.117879  0.47
2007 Trylska J, Tozzini V, Chang CE, McCammon JA. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophysical Journal. 92: 4179-87. PMID 17384072 DOI: 10.1529/Biophysj.106.100560  0.479
2007 Chang CE, Trylska J, Tozzini V, McCammon JA. Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chemical Biology & Drug Design. 69: 5-13. PMID 17313452 DOI: 10.1111/J.1747-0285.2007.00464.X  0.545
2007 Chang CE, Chen W, Gilson MK. Ligand configurational entropy and protein binding. Proceedings of the National Academy of Sciences of the United States of America. 104: 1534-9. PMID 17242351 DOI: 10.1073/Pnas.0610494104  0.601
2007 Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. Journal of Structural Biology. 157: 606-15. PMID 17029846 DOI: 10.1016/J.Jsb.2006.08.005  0.489
2006 Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA. The influence of macromolecular crowding on HIV-1 protease internal dynamics. Journal of the American Chemical Society. 128: 6006-7. PMID 16669648 DOI: 10.1021/Ja060483S  0.473
2006 Chen W, Chang CE, Gilson MK. Concepts in receptor optimization: targeting the RGD peptide. Journal of the American Chemical Society. 128: 4675-84. PMID 16594704 DOI: 10.1021/Ja056600L  0.573
2006 Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophysical Journal. 90: 3880-5. PMID 16533835 DOI: 10.1529/Biophysj.105.074575  0.514
2005 Chang CE, Chen W, Gilson MK. Evaluating the Accuracy of the Quasiharmonic Approximation. Journal of Chemical Theory and Computation. 1: 1017-28. PMID 26641917 DOI: 10.1021/Ct0500904  0.563
2005 Minh DD, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophysical Journal. 89: L25-7. PMID 16100267 DOI: 10.1529/Biophysj.105.069336  0.51
2004 Chang CE, Gilson MK. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. Journal of the American Chemical Society. 126: 13156-64. PMID 15469315 DOI: 10.1021/Ja047115D  0.596
2004 Chen W, Chang CE, Gilson MK. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophysical Journal. 87: 3035-49. PMID 15339804 DOI: 10.1529/Biophysj.104.049494  0.614
2003 Chang CE, Gilson MK. Tork: Conformational analysis method for molecules and complexes. Journal of Computational Chemistry. 24: 1987-98. PMID 14531053 DOI: 10.1002/Jcc.10325  0.523
2003 DeJong ES, Chang CE, Gilson MK, Marino JP. Proflavine acts as a Rev inhibitor by targeting the high-affinity Rev binding site of the Rev responsive element of HIV-1. Biochemistry. 42: 8035-46. PMID 12834355 DOI: 10.1021/Bi034252Z  0.583
2003 Chang CE, Potter MJ, Gilson MK. Calculation of molecular configuration integrals Journal of Physical Chemistry B. 107: 1048-1055. DOI: 10.1021/Jp027149C  0.521
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