RECENT PUBLICATIONS
CaXML: CHEMISTRY-INFORMED MACHINE LEARNING EXPLAINS MUTUAL CHANGES BETWEEN PROTEIN CONFORMATIONS AND CALCIUM IONS IN CALCIUM-BINDING PROTEINS USING STRUCTURAL AND TOPOLOGICAL FEATURES
Pengzhi Zhang,Jules Nde Yossi Eliaz Nathaniel Jennings,Piotr Cieplak, Margaret. S. Cheung, submitted (2024).
POTENTIAL QUANTUM ADVANTAGE FOR SIMULATION OF FLUID DYNAMICS
X. Li, X. Yin, N. Wiebe, J. Chun, G. K. Schenter, M. S. Cheung, J. Muelmenstaedt, accepted by Physical Review Research (2024).
IMPROVED ENZYME FUNCTIONAL ANNOTATION PREDICTION USING CONTRASTIVE LEARNING WITH STRUCTURAL INFERENCE
Y. Yang, A. Jerger, S. Feng, Z. Wang, C. Brasfield, M. S. Cheung, J. Zucker, Q. Guan , accepted by Communications Biology (2024)
PTM-PSI: A PYTHON PACKAGE TO FACILITATE THE COMPUTATIONAL INVESTIGATION OF POST-TRANSLATIONAL MODIFICATION ON PROTEIN STRUCTURES AND THEIR IMPACTS ON DYNAMICS AND FUNCTIONS
Daniel Mejia-Rodriguez*, Hoshin Kim*, Natalie Sadler, Xiaolu Li, Pavlo Bohutskyi, Marat
Valiev, Wei-Jun Qian, Margaret S. Cheung, Protein Science, 32, e4822, Protein Science (2023).
EXPERIMENT AND SIMULATION REVEAL RESIDUE DETAILS FOR HOW POLYMORPHOUS TARGET BINDING TUNES CALMODULIN'S CALCIUM-BINDING PROPERTIES
J. Nde, P. Zhang, M. N. Waxham, M. S. Cheung, J. Phys. Chem. B, 127, 2900-2908 (2023).
GRAPH IDENTIFICATION OF PROTEINS IN TOMOGRAMS (GRIPTOMO)
A. George, D. N. Kim, T. Moser, I. T. Gildrea, J. Evans, M. S. Cheung, Protein Science, 32, e4538 (2023).
EFFECTS OF PROTEIN CROWDERS AND CHARGE ON THE FOLDING OF SUPEROXIDE DISMUTASE 1 VARIANTS: A COMPUTATIONAL STUDY
A. Sarkar, A. G. Gasic, M. S. Cheung, and G. C. Morrison, J. Phys. Chem. B. 126, 4458-4471(2022).
A GENERALIZED FLORY-STOCKMAYER KINETIC THEORY OF CONNECTIVITY PERCOLATION AND RIGIDITY PERCOLATION OF CYTOSKELETAL NETWORK
C. Bueno, J. Liman, N. P. Schafer, M. S. Cheung, P. G. Wolynes, PoLS Comp. Biol. 18, e1010105 (2022).
CORRELATING INTERFACIAL CHARGE TRANSFER RATES WITH INTERFACIAL MOLECULAR STRUCTURE IN THE TETRAPHENYLDIBENZOPERIFLANTHENE/C70 ORGANIC PHOTOVOLTAIC SYSTEM
J. Tinnin, S. Bhandari, P. Zhang, E. Geva, B. D. Dunietz, X. Sun, M. S. Cheung. J.P.C. Letters, 13, 763-769 (2022)
FORECASTING AVALANCHES IN BRANCHED ACTOMYOSIN NETWORKS WITH NETWORK SCIENCE AND MACHINE LEARNING
C. Li, J. Liman, Y. Eliaz, M. S. Cheung, J. Phys. Chem. B, 125, 11591-11605 (2021)
CTRAMER: SOFTWARE FOR CALCULATING CHARGE-TRANSFER-RATE CONSTANTS WITH CONDENSED-PHASE EFFECTS
J. Tinnin, S. Bhandari, P. Zhang, H. Aksu, B. Maiti, E. Geva, B. D. Dunietz, X. Sun, M. S. Cheung, J. Chem. Phys. 154, 214108 (2021).
COARSE-GRAINED MODELING AND MOLECULAR DYNAMICS SIMULATIONS OF CA2+-CALMODULIN
J. Nde, P. Zhang, J. C. Ezerski, P. G. Wolynes, M. S. Cheung, Frontiers in Molecular Sciences, 8, 661322 (2021)
DETERMINING THE ATOMIC CHARGE OF CALCIUM ION IN A CALCIUM-BINDING PROTEIN REQUIRES THE INFORMATION OF ITS DYNAMIC COORDINATION GEOMETRY IN AQUEOUS SOLUTION
P. Zhang, J. Han, P. Cieplak, M. S. Cheung, J. Chem. Phys. 154, 124104 (2021).
UNDERSTANDING PROTEIN-COMPLEX ASSEMBLY THROUGH GRAND CANONICAL MAXIMUM ENTROPY MODELING
Andrei G. Gasic, Atrayee Sarkar, and Margaret S. Cheung Phys. Rev. Research, 3, 033220 (2021)
THE ZERO-ORDER LOOP IN APOAZURIN MODULATES UNFOLDING IN SILICO
F. C. Zegarra, D. Homouz, P. Wittung-Stafshede, M. S. Cheung, J. Phys. Chem. B, 125, 3501-3509 (2021)