I am a computer-aided drug design (CADD) expert with 18 years of drug discovery experience spanning pharmaceutical and biotech companies, with multiple programs advancing to candidate selection and human clinical trials. My expertise encompasses target virtual screening of ultra-large chemical libraries, tractability assessment, hit identification and optimization, protein structure prediction and construct design, and physicochemical/ADMET property prediction – areas central to modern drug discovery. For the past four years, I have focused on small molecule precision oncology, tackling some of the most difficult targets in the field, including oncogenic missense mutants (e.g., KRAS and p53 variants) and transcription factors (e.g., POU2F3). Throughout my career, I have demonstrated excellence at identifying novel solutions for the right questions and extracting actionable mechanistic insights through close collaboration between experimental and computational teams. I look forward to leveraging my deep industry experience at the lab to drive innovations in CADD technologies and to push the frontier of computational drug discovery by utilizing the state-of-the-art HPC infrastructure as well as the cutting-edge machine learning expertise at LLNL. 

Ph.D. Chemistry, Stony Brook University, Stony Brook, New York

M.S. Chemistry, Institute of Chemistry, the Chinese Academy of Sciences, Beijing, China

B.S. Chemistry, University of Science and Technology of China, Hefei, China

Cui, G., et al. GRAM: A True Null Model for Relative Binding Affinity Predictions. Journal of Chemical Information and Modeling, vol. 60, no. 1, Jan. 2020, pp. 11-16. ACS Publications, doi:10.1021/acs.jcim.9b00939.

Spletstoser, J.T., Dreabit, J., Knox, A.N., Benowitz, A., Campobasso, N., Ward, P., Cui, G., Lewandowski, T., McCloskey, L., and Aubart, K.M., Discovery of pipierazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections, Bioorganic & Medicinal Chemistry Letters, 2019, 29 (16):2410-2414.

Graves, A.P., Wall, I.D., Edge, C.M., Woolven J.M., Cui, G., Le Gall, A., Hong X., Raha, K., and Manas, E.S., A perspective on water site prediction methods for structure based drug design, Current Topics in Medicinal Chemistry, accepted, 2017

Carlson, H.A., Smith, R.D., Damm-Ganamet, K.L., Stuckey, J.A., Ahmed, A., Convery, M.A., Somers, D.O., Kranz, M., Elkins, P.A., Cui, G., Peishoff, C.E., Lambert, M.H., Dunbar Jr., J.B., CSAR 2014: a Benchmark Exercise Using Unpublished Data from Pharma, Journal of Chemical Information and Modeling, 2016, 56 (6):1063-1077.

Gilmartin, A., Faitg, T., Richter, M.C., Groy, A., Mark, S., Darcy, M.G., Peng, X., Fisher, K.E., Yang, J., Zhang, S., Minthorn, E., Jaworski, J. -P., Schaber, M.D., Martens, S., McNulty, D.E., Sinnamon, R.H., Zhang, H., Kirkpatrick, R., Nevins, N., Cui, G., Pietrak, B., Diaz, E., Jones, A.D., Brandt, M., Schwartz, B., Heerding, D., and Kumar, R., A novel class of allosteric inhibitors of the oncogenic Wip1 phosphatase. Nature Chemical Biology, 2014, 10 (3):181-187.

Cui, G., Swails, J.M., and Manas, E.S., SPAM: a simple approach for profiling bound water molecules. Journal of Chemical Theory and Computation, 2013, 9 (12):5539-5549.

Rubach, J.K., Cui, G., Schneck, J.L., Taylor, A.N., Zhao, B., Smallwood, A., Nevins, N., Wisnoski, D., Thrall, S.H., and Meek, T.D., The amino-acid substitutions of dipeptide substrates of cathepsin C can determine the rate-limiting steps of catalysis. Biochemistry 2012, 51 (38):7551-7568.

Yang, Y.,Wang, B., Ucisik, M.N., Cui, G., Fierke, C.A., and Merz, K.M., Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. Journal of the American Chemical Society 2011, 134 (2):820-823.9. Cui, G., Li, X., Yu, N., and Merz, K.M., Interpreting the observed substrate selectivity and the product regioselectivity in Orf2-catalyzed prenylation from X-ray structures, Multi-scale Quantum Models for Biocatalysis – Challenges and Advances in Computational Chemistry and Physics, 2009, 7:351-375.

He, X., Fusti-Molnar, L., Cui, G., and Merz, K.M., Importance of dispersion and electron correlation in ab initio protein folding, Journal of Physical Chemistry B, 2009, 113 (15):5290-5300.

Cui, G. and Merz, K.M., The Intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis. Biophysical Journal, 2008, 94 (10):3769-3778.

Cui, G. and Merz, K.M., Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate. Biochemistry, 2007, 46 (43):12375-12381.

Riley, K.E., Cui, G., and Merz, K.M., An ab initio investigation of the interactions involving the aromatic group of the set of fluorinated N-(4-sulfamylbenzoyl)benzylamine inhibitors and human carbonic anhydrase II. Journal of Physical Chemistry B, 2007, 111 (20):5700-5707.

Okur, A., Roe, D., Cui, G., Hornak, V., and Simmerling, C., Improving convergence of replica exchange simulations through coupling to a high-temperature structure reservoir. Journal of Chemical Theory and Computation, 2007, 3 (2):557-568.

Cui, G., Li, X., and Merz, K.M., Understanding the substrate selectivity and the product regioselectivity of Orf2-catalyzed aromatic prenylations. Biochemistry, 2007, 46 (5):1303-1311.

Yu, N., Li, X., Cui, G., Hayik, S.A., and Merz, K.M., Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Protein Science, 2006, 15 (12):2773-2784.

Wang, P. -F., Flynn, A.J., Naor, M.M., Jensen, J.H., Cui, G., Merz, K.M., Kenyon, G.L., and McLeish, M.J., Exploring the role of the active site cysteine in human muscle creatine kinase. Biochemistry, 2006, 45 (38):11464-11472.

Rafi, S.B., Cui, G., Song, K., Cheng, X., Tonge, P.J., and Simmerling, C., Insight through molecular mechanics Poisson-Boltzmann surface area calculations into the binding affinity of triclosan and three analogues for FabI, the E. coli enoyl reductase. Journal of Medicinal Chemistry, 2006, 49 (15):4574-4580.

Zuo, X., Cui, G., Merz, K.M., Zhang, L., Lewis, F.D., and Tiede, D.M., X-ray diffraction “fingerprinting” of DNA structure in solution for quantitative evaluation of molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103 (10):3534-3539.

Cui, G., Wang, B., and Merz, K.M., Computational studies of the farnesyltransferase ternary complex part I: substrate binding. Biochemistry, 2004, 44 (50):16513-16523.

Cheng, X., Cui, G., Hornak, V., and Simmerling, C., Modified replica exchange simulation methods for local structure refinement. Journal of Physical Chemistry B, 2004, 109 (16):8220-8230.

Cui, G., and Simmerling, C., Conformational heterogeneity observed insimulations of a pyrene-substituted DNA. Journal of the American Chemical Society, 2002, 124 (41):12154-12164.

Oral Presentations

Cui, G., Importance sampling: from free energy calculations to machine learning, Openeye CUP 2019, Santa Fe, NM

Cui, G., Assessing Relative Binding Free Energy Predictions: from Null Model to Null System, Free Energy Workshop in Drug Design, 2018, Boston, MA

Cui, G., Affinity predictions with FEP+: a different perspective on performance and utility, Workshop on Free Energy Methods in Drug Design, 2016, Boston, MA (invited, doi: 10.7490/f1000research.1112773.1)

Cui, G., Protein-ligand recognition: insights from a thermodynamic measure of local solvation, The 248th ACS National Meeting, August 2014, San Francisco, CA. (invited)

Cui, G., SPAM – a simple approach for profiling bound water molecules, Workshop on Free Energy Methods in Drug Design, 2012, Cambridge, MA. (invited)

Sharad, V., Lafrance, L.V., Li, M., Duquenne, C., Cui, G., Miller, W., Smallwood, A., Zhao, B., McDevitt, P.J., Key, D.E., Hou, W., Gontarek, R.R., Johnson, N., and Cecconie, T.J., Identification and synthesis of benzimidazole carboxamides as potent inhibitors of focal adhesion kinase (FAK), American Association of Cancer Research, 2011, Orlando, FL.

Price, A.T., Szewczuk, L., Holmes, D., Cui, G., and Elkins, P.A., Identification of the first potent inhibitors of tRNA (m1G37) methyltransferase (TrmD) via an integrated screening approach, SERMACS 2012, Raleigh, NC.

Cui, G., Li, X., and Merz, K.M., The alternative binding in Orf2 catalyzed prenylation: identification and validation, The 233rd ACS National Meeting, March 2007, Chicago, IL.

Cui, G., Quantum-mechanics flavored scoring function for protein structure prediction, The 3rd UCSC/QB3 Symposium on Bioinformatics, 2006, Santa Cruz, CA.

Cui, G., Farnesyltransferase, the 7-angstrom gap and intermediate states, The 46th Sanibel Symposium, 2006, St. Simons Island, GA.

Cui, G., Constrained molecular dynamics simulations with AMBER, AMBER Developers Meeting, 2005, University of Utah, Salt Lake City, Utah.

Cui, G., Coarse-grain modeling with AMBER, AMBER Developers Meeting, 2004, Stony Brook University, Stony Brook, NY.

Cui, G., Implementation of replica exchange method in AMBER, AMBER Developers Meeting, 2003, The Scripps Research Institute, La Jolla, CA.

Okur, A., Roe, D.R., Cui, G., Hornak, V., and Simmerling, C., Folding kinetics of a beta-hairpin: a molecular dynamics study. Abstract of Papers of the American Chemical Society 2003, 226, U450-U451.

Cui, G., Roitberg, A.E., and Simmerling, C., Unified kinetic and thermodynamic simulation study of the complex folding landscape for an all-atom model peptide in solution. Abstract of Papers of the American Chemical Society 2003, 225, U765-U765.16. Cui, G. and Simmerling, C., The convergence studies of replica exchange method and its implementation in AMBER, Gordon Research Conference (Computational Chemistry) 2002, Colby-Sawyer College, NH

Cui, G. and Simmerling, C., Syn or anti: molecular dynamics studies of an underdetermined DNA structure, Peter A. Kollman Memorial Symposium 2002, UCSF, San Francisco, CA.