Publications

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Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.
Nan Y, Baral P, Orr AA, Michel HM, Lemkul JA, MacKerell AD. 2024. Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems. The journal of physical chemistry. B : . DOI: 10.1021/acs.jpcb.4c06354
Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens.
Wu D, Yin R, Chen G, Ribeiro-Filho HV, Cheung M, Robbins PF, Mariuzza RA, Pierce BG. 2024. Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens. Science advances 10(47): eadq6150. DOI: 10.1126/sciadv.adq6150
Toripalimab Plus Chemotherapy as a First-Line Therapy for Extensive-Stage Small Cell Lung Cancer: The Phase 3 EXTENTORCH Randomized Clinical Trial.
Cheng Y, Zhang W, Wu L, Zhou C, Wang D, Xia B, Bi M, Fu X, Li C, Lv D, et al. 2024. Toripalimab Plus Chemotherapy as a First-Line Therapy for Extensive-Stage Small Cell Lung Cancer: The Phase 3 EXTENTORCH Randomized Clinical Trial. JAMA oncology : . DOI: 10.1001/jamaoncol.2024.5019
Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.
Teng X, Yu W, MacKerell AD. 2024. Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c00966
Biomimetic Redox Capacitor To Control the Flow of Electrons.
Kim E, Zhao Z, Wu S, Li J, Bentley WE, Payne GF. 2024. Biomimetic Redox Capacitor To Control the Flow of Electrons. ACS applied materials & interfaces : . DOI: 10.1021/acsami.4c13032
modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.
Love O, Galindo-Murillo R, Roe DR, Dans PD, Cheatham Iii TE, Bergonzo C. 2024. modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c01164
A fitness distribution law for amino-acid replacements.
Sun M, Stoltzfus A, McCandlish DM. 2024. A fitness distribution law for amino-acid replacements. bioRxiv : the preprint server for biology : . DOI: 10.1101/2024.10.11.617952
A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV.
Sajadi MM, Abbasi A, Tehrani ZR, Siska C, Clark R, Chi W, Seaman MS, Mielke D, Wagh K, Liu Q, et al. 2024. A comprehensive engineering strategy improves potency and manufacturability of a near pan-neutralizing antibody against HIV. bioRxiv : the preprint server for biology : . DOI: 10.1101/2024.10.14.618178
Engineering GID4 for use as an N-terminal proline binder via directed evolution.
Ikonomova SP, Yan B, Sun Z, Lyon RB, Zatopek KM, Marino JP, Kelman Z. 2024. Engineering GID4 for use as an N-terminal proline binder via directed evolution. Biotechnology and bioengineering : . DOI: 10.1002/bit.28868
Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.
J N C, Guvench O, MacKerell AD, Yamaguchi T, Mallajosyula SS. 2024. Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy. Journal of chemical theory and computation : . DOI: 10.1021/acs.jctc.4c00656
Exploring the potential of structure-based deep learning approaches for T cell receptor design.
Ribeiro-Filho HV, Jara GE, Guerra JVS, Cheung M, Felbinger NR, Pereira JGC, Pierce BG, Lopes-de-Oliveira PS. 2024. Exploring the potential of structure-based deep learning approaches for T cell receptor design. PLoS computational biology 20(9): e1012489. DOI: 10.1371/journal.pcbi.1012489
Exploring Druggable Binding Sites on the Class A GPCRs Using the Residue Interaction Network and Site Identification by Ligand Competitive Saturation.
Inan T, Yuce M, MacKerell AD, Kurkcuoglu O. 2024. Exploring Druggable Binding Sites on the Class A GPCRs Using the Residue Interaction Network and Site Identification by Ligand Competitive Saturation. ACS omega 9(38): 40154-40171. DOI: 10.1021/acsomega.4c06172
TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions.
Lin V, Cheung M, Gowthaman R, Eisenberg M, Baker BM, Pierce BG. 2024. TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions. Nucleic acids research : . DOI: 10.1093/nar/gkae840
Hydrolytically Degradable Zwitterionic Polyphosphazene Containing HEPES Moieties as Side Groups.
Tagad HD, Marin A, Hlushko R, Andrianov AK. 2024. Hydrolytically Degradable Zwitterionic Polyphosphazene Containing HEPES Moieties as Side Groups. Biomacromolecules : . DOI: 10.1021/acs.biomac.4c01008
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, et al. 2024. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B : . DOI: 10.1021/acs.jpcb.4c04100