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Welcome to the YSL Group

We are a computational chemistry group working towards a better understanding of the structures and functions of biomolecules.

About the YSL Group

The YSL Group aims to elucidate the structures and functions of biomolecules by integrating the power of advanced computations with the elegance of chemical theory. Our focus is to develop and apply computational methodology to significant biological problems that are difficult to address experimentally. Two major research projects in the YSL Group are (1) to understand and design cyclic peptides with desired conformations to modulate protein–protein interactions and (2) to elucidate the structural and functional roles of post-translational modifications and non-natural amino acids on protein folding.

Our group meetings in Summer 2023 are Friday at 12 pm.
For more details, please email YSL at yu-shan.lin@tufts.edu

Our Research

The YSL Group seeks to model structure prediction for cyclic peptides using molecular dynamics simulations and enhanced sampling methods.

Our team works to understand the effects of post-translational modifications and non-natural amino acids on protein folding.

The Lin lab aims to develop effective techniques for unsupervised analysis of molecular dynamics simulation trajectories and other noisy time series.

Papers by YSL

Outreach

Resources

News from the YSL Group

2022

November 2023
Our paper “Computational prediction of cyclic peptide structural ensembles and application to the design of Keap1 binders,” with the Kritzer Lab at Tufts is published in J. Chem. Inf. Model.
June 2023
Francini Fonseca Lopez defends her PhD thesis. Congratulations, Francini!
May 2023
Marc Descoteaux completed his 4+1 program and graduated with a M.S. in Materials Science and Engineering. Congratulations, Marc!
May 2023
Our paper “Training neural network models using molecular dynamics simulation results to efficiently predict cyclic hexapeptide structural ensembles,” is published in J. Chem. Theory Comput.
May 2023
Jovan Damjanovic defends his PhD thesis. Congratulations, Jovan!

Postdoc Positions Available

We are looking for two computational chemists experienced in machine learning and peptide molecular dynamics simulations to join us and work on cyclic peptide design or simulation analysis method development. Must have a strong background in machine learning methods and extensive experience in their applications; experience with enhanced sampling methods, GROMACS, and PLUMED a plus.

If you are interested or know someone who might be interested, please send along (or have them send along) a CV and a couple of relevant publications to Prof. Lin at yu-shan.lin@tufts.edu

Graduate Students Interested in the YSL Group

Although some modeling or simulation experience is great, you don’t need to have prior computational chemistry experience to join our group! We will train you from the beginning and get you up to speed. As long as you like peptides and proteins and are not afraid of math, physics, and computers, we will get you there! Feel free to reach out to Prof. Lin and any graduate students in the group. You can find their emails here.

Undergraduate Students Interested in the YSL Group

For Tufts undergraduate students (first-years or sophomores) who are interested in the YSL Group, please apply on the chemistry department website here.

For other research opportunities in the Chemistry Department: Check out the chemistry faculty members’ research websites. You can find them here.

For other research opportunities in computational science at Tufts: Look up Tim Atherton in Physics, Lenore Cowen and Soha Hassoun in Computer Science, and Prashant Deshlahra in Chemical and Biological Engineering.