Publications

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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
Yersinia pseudotuberculosis growth arrest during type-III secretion system expression is associated with altered ribosomal protein expression and decreased gentamicin susceptibility.
Greene J, Snyder RA, Cotten KL, Huiszoon RC, Chu S, Braza RED, Chapin AA, Stine JM, Bentley WE, Ghodssi R, et al. 2024. <i>Yersinia pseudotuberculosis</i> growth arrest during type-III secretion system expression is associated with altered ribosomal protein expression and decreased gentamicin susceptibility. bioRxiv : the preprint server for biology : . DOI: 10.1101/2024.09.02.610769
First-in-Class Mitogen-Activated Protein Kinase p38α: MAPK-Activated Protein Kinase-2 (MK2) Dual Signal Modulator with Anti-inflammatory and Endothelial-stabilizing Properties.
Tulapurkar ME, Shirey KA, Lugkey KN, Luo W, Lal R, Galan A, Mahmoud O, McClean N, Thangaraju K, Cericola D, et al. 2024. First-in-Class Mitogen-Activated Protein Kinase p38α: MAPK-Activated Protein Kinase-2 (MK2) Dual Signal Modulator with Anti-inflammatory and Endothelial-stabilizing Properties. The Journal of pharmacology and experimental therapeutics : . DOI: 10.1124/jpet.124.002281
Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.
Nordquist EB, Zhao M, Kumar A, MacKerell AD. 2024. Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots. Journal of chemical information and modeling : . DOI: 10.1021/acs.jcim.4c01189
Electrobiofabrication of antibody sensor interfaces within a 3D printed device yield rapid and robust electrochemical measurements of titer and glycan structure.
Chen CY, Motabar D, Zakaria FR, Kim E, Wu B, Payne GF, Bentley WE. 2024. Electrobiofabrication of antibody sensor interfaces within a 3D printed device yield rapid and robust electrochemical measurements of titer and glycan structure. Biotechnology and bioengineering : . DOI: 10.1002/bit.28839
Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models.
Hatch HW, Bergonzo C, Blanco MA, Yuan G, Grudinin S, Lund M, Curtis JE, Grishaev AV, Liu Y, Shen VK. 2024. Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models. The Journal of chemical physics 161(9): . DOI: 10.1063/5.0224809