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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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Categories

  • Papers (12)
  • News (26)
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People

  • Dr. David L. Mobley
  • PostDoc
    • Lea El Khoury
    • Sukanya Sasmal
  • Graduate
    • Nathan M. Lim
    • Camila Zanette
    • Guilherme D. R. Matos
    • Caitlin C. Bannan
    • Sam Gill
    • Victoria Lim
    • Kalistyn Burley
    • David Wych
    • Jessica Maat
  • Undergraduate
    • Linh Nguyen
    • Meghan Osato
    • Jordan Ehrman

Recent Papers

Escaping Atom Types in Force Fields Using Direct Chemical Perception

David L. Mobley , Caitlin C. Bannan , Andrea … [Read More...]

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

Guilherme Duarte Ramos Matos, David L. … [Read More...]

SAMPL6 challenge results from pKa predictions based on a general Gaussian process model

Caitlin C. Bannan, David L. Mobley, A. Geoffrey … [Read More...]

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

David Mobley, Caitlin C. Bannan, Andrea Rizzi, … [Read More...]

Binding modes of ligands using enhanced sampling (BLUES)

Samuel C. Gill, Nathan M. Lim, Patrick B. … [Read More...]

RSS What we’re reading:

  • Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigor February 20, 2019
  • Biomolecular force fields: where have we been, where are we now, where do we need to go and how do w February 20, 2019
  • Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM ad February 19, 2019
  • Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanc February 19, 2019
  • Minnesota Solvation Database February 9, 2019

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Contact

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

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