Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Nathan M. Lim

Biography

Nathan Lim completed his B.S. in Pharmaceutical Sciences from the University of California, Irvine in 2014. His undergraduate research career consisted of work in 2 separate labs, under Dr. Mobley and Dr. Poulos. In the Poulos lab, he did protein crystallography work on nitric oxide synthase . Research in the Mobley lab focused on applied methods of computational chemistry to predict protein-ligand binding affinities, binding mode, and solvation free energies . For summer 2014, he worked in program development to predict protein-ligand binding free energies as an intern at Schrödinger in New York. Then, he re-joined the Mobley lab as a graduate student in Fall 2014 under the Pharmacological Sciences Ph.D. program to continue his research and apply computational techniques to guide drug-design projects. In Summer 2015, he returned for another Schrödinger summer internship to study the sensitivity of binding free energy predictions due to protein conformational changes . During the 2015-2016 academic year, he was awarded the 2015 NSF Graduate Research Fellowship. His graduate research revolves around using molecular simulations for studying protein-membrane systems , predicting protein-ligand binding modes and affinities. His primary focus is on developing the software behind an enhanced sampling method called BLUES  and contributing to the development of OpenEye Scientific’s Orion cloud computing platform to accelerate drug discovery efforts. He was awarded the Molecular Software Sciences Institute Phase-I Software Fellowship on July 2018.

LimNathan-CV_2018-08 (Last Updated: August 30th, 2018)

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(1)
Lim, N. M.; Wang, L.; Abel, R.; Mobley, D. L. Sensitivity in Binding Free Energies Due to Protein Reorganization. Journal of Chemical Theory and Computation 2016, 12 (9), 4620–4631. https://doi.org/10.1021/acs.jctc.6b00532.
(1)
Holden, J. K.; Lim, N. M.; Poulos, L. Identification of Redox Partners and Development of a Novel Chimeric Bacterial Nitric Oxide Synthase for Structure Activity Analyses. Journal of Biological Chemistry 2014, 289 (42), 29437–29445. https://doi.org/10.1074/jbc.M114.595165.
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Holden, J. K.; Kang, S.; Hollingsworth, S. A.; Li, H.; Lim, N.; Chen, S.; Huang, H.; Xue, F.; Tang, W.; Silverman, R. B.; et al. Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors. Journal of medicinal chemistry 2015, 58 (2), 994–1004. https://doi.org/10.1021/jm501723p.
(1)
Mobley, D. L.; Wymer, K. L.; Lim, N. M.; Guthrie, J. P. Blind Prediction of Solvation Free Energies from the SAMPL4 Challenge. Journal of Computer-Aided Molecular Design 2014, 28, 135–150. https://doi.org/10.1007/s10822-014-9718-2.
(1)
Mobley, D. L.; Liu, S.; Lim, N. M.; Wymer, K. L.; Perryman, A. L.; Forli, S.; Deng, N.; Su, J.; Branson, K.; Olson, A. J. Blind Prediction of HIV Integrase Binding from the SAMPL4 Challenge. Journal of Computer-Aided Molecular Design 2014, 28 (4), 327–345. https://doi.org/10.1007/s10822-014-9723-5.
(1)
Liu, S.; Wu, Y.; Lin, T.; Abel, R.; Redmann, J. P.; Summa, C. M.; Jaber, V. R.; Lim, N. M.; Mobley, D. L. Lead Optimization Mapper: Automating Free Energy Calculations for Lead Optimization. Journal of Computer-Aided Molecular Design 2013, 27 (9), 755–770. https://doi.org/10.1007/s10822-013-9678-y.
(1)
Gill, S. C.; Lim, N. M.; Grinaway, P. B.; Rustenburg, A. S.; Fass, J.; Ross, G. A.; Chodera, J. D.; Mobley, D. L. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. J. Phys. Chem. B 2018. https://doi.org/10.1021/acs.jpcb.7b11820.
(1)
Kyrychenko, A.; Lim, N. M.; Vasquez-Montes, V.; Rodnin, M. V.; Freites, J. A.; Nguyen, L. P.; Tobias, D. J.; Mobley, D. L.; Ladokhin, A. S. Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. The Journal of Membrane Biology 2018. https://doi.org/10.1007/s00232-018-0030-2.

 

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David L. Mobley
dmobley@mobleylab.org
phone: 949.385.2436
office: 3134B Nat. Sci. I

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