Peng He Email & Phone Number

Wilmington, Delaware, United States

In my role at Incyte, I provided computational support to different drug discovery projects, employing techniques like Ligand-Based methods, Homology Modeling, Docking, FEP+, and Quantum Mechanical methods for high-throughput screening and lead optimization.My responsibilities also encompassed the evaluation and incorporation of various computational methodologies, including WaterMap/SSTMap, Glide_EM/Phenix_OPLS, Orion_NES, and other FEP softwares.

Chicago, Illinois, United States

I applied various coarse-graining methods to correlate the predicted assembly of large-scale molecular structures with the design of their molecular building blocks. My studies have involved the molecular assembly of diverse protein-based mega-molecules through coarse-grained molecular modeling and simulation. Notably, I conducted computational predictions of NTD-CTD and CTD-RNA interaction interfaces in SARS-CoV-2's vRNP using Molecular Dynamic simulations. In collaboration with Eli Lilly, I've also utilized advanced coarse-grained modeling and simulation techniques to predict mAbs' viscosity.

Greater Philadelphia Area

My research is primarily devoted to the development of novel free energy methods, large-scale host-guest binding free energy calculations, and the study of molecular recognition principles. I undertake conformational analyses and free energy calculations to assess the properties of disease-related proteins and their respective inhibitors. This includes conformational free energy calculations and binding affinity/specificity evaluations utilizing a variety of computational methods.My work includes the study of the basis of molecular recognition by large-scale host-guest binding free energy calculations. I've also focused on understanding kinase states, clustering new inactive conformational states, and identifying the influence of critical inhibitor features on selective binding. Moreover, I present the intrinsic selectivity of type II inhibitors based on disparities in kinase conformational propensities.My work extends to binding affinity predictions of inhibitors with HIV-integrase, HIV-protease, and kinases. I have successfully improved the prediction of false positives for HIV-protease inhibitors using free energy methods. Notably, my team achieved the second-best enrichment in the SAMPL4: HIV-integrase LEDGF binding prediction competition. We have also predicted the binding affinity of MAP4K4 inhibitors via docking and free energy methods.A significant part of my research is the development and implementation of the Restrain-Free Energy Perturbation-Release (R-FEP-R) method. I have optimized the simulation protocol for R-FEP-R, and validated the selective binding of two similar ligands to different kinase conformations through both the R-FEP-R method and conventional FEP calculations

New Jersey

My research in this period focuses on investigating the basic thermodynamics of molecular binding especially free energy calculation and solvation effects using molecular modeling and dynamics tools.

Doctor Of Philosophy - Phd, Computational Biochemistry

Ph.D., Chemistry

B.S., Chemistry