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Lin Li
Lin Li
University of Texas at El Paso
United States
Biography
Education and work experience:
•Research Associate (Biophysics), Clemson University, 2013-now
•Post Doct (Biophysics), Clemson University, 2011-2013
•Ph.D. (Biophysics), Huazhong University of Science and Technology, 2005-2011
Research experience:
DelPhi Development: DelPhi is a widely used Poisson Boltzmann Equation solver. I have developed a Gaussian smooth method to DelPhi software, which is used to model the inhomogeneous dielectric properties of macromolecules. This method has been proved to be more accurate than the traditional 2-dielectric constant methods.
MEMPOT: A Membrane Potential (MEMPOT) tool is developed and implemented into DelPhi program. Using this MEMPOT tool, one can easily calculate the electrostatic potential distribution across the membrane.
ASPDock: He have developed a docking algorithm (ASPDock) to calculate binding free energy of protein complexes, which improves the accuracy of prediction effectively. Comparisons with other state-of-the-art docking algorithms showed that ASP score indeed gives higher success rate than the pure shape complementarity score of FTDock.
SRM: He also developed a Softly Restricting Method (SRM), which utilizes the unreliable binding site information to enhance success rate of docking. It only reduces hit count number and success rate slightly if the predicted information is completely wrong. However, when the predicted information is correct or partially correct, SRM increases the hit count number and success rate significantly.
CAPRI: Using ASPDock and Softly Restricting Method, his team has participated in two rounds of Critical Assessment of PRediction of Interactions (CAPRI). We got high-quality hits for T40 and T41 and the best LRMSD were 2.35 Å and 1.41 Å, respectively.
Awards:
2001-2002: HUST Scholarship
2002-2003: National Scholarship by Chinese Government
Skills and Software
Programming language: Fortran/C/C++/Bash/Matlab
Molecular Simulatons: DelPhi/Tinker /NAMD
Protein-protein docking: ASPDock/SRM/FTDock/ZDOCK/GRAMM
Graphic: Chimera/PyMOL/Photoshop/Flash
Homology Modeling: SWISS-MODEL/I-TASSER
Research Interest
1.Protein electrostatic calculations ;
2.Molecular dynamic simulations;
3.Protein-protein interactions, Protein-RNA/DNA interactions, Protein-ligand docking;
4.Structure, function, chemistry, and in vivo modification and processing of proteins, nucleic acids, and other biologically important macromolecules;
5.Computational method for protein/DNA/RNA simulations.
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