Yi He Laboratory

Computer modeling of Biomolecules 


My first Ph.D. student, Amy Stevens, has successfully defended her thesis, and I am so proud of her.

I would like to extend my gratitude to the exceptional committee for guiding her toward success.



 2024-03-19  Congratulations to Shenghan for successfully defending his Ph.D. thesis. I am thrilled that he has come this far and earned his Ph.D. in my group at UNM. I hope he will continue to pursue his interests in aerosol research. Take note of the legendary committee behind Shenghan!


2024-03-09 Take a look at this dedicated team, ready to host high school students who will compete in the U.S. National Chemistry Olympiad's local chapter from various parts of New Mexico. It was a pleasure to meet all of the students and share our research with them through Virtual Reality, as well as showcase our 50-GPU cluster.


2024-03-06  Congratulations to Tongtong, who has done an outstanding job presenting her research over the past years and successfully defended her Ph.D. thesis. I am so proud of her and wish her all the success in her pursuit of a faculty career in the future. 


2024-02-01 Congratulations to Shenghan whose manuscript titled "High UV damage and low repair, but not cytosine deamination, stimulate mutation hotspots at ETS binding sites in melanoma" has been published by PNAS

2024-01-23 Finally, the Center for Computational Chemistry's website is now online. More information is coming! Check it out at https://ccc.unm.edu/


2023-11-30 Dr. He has finished his tenure tour, done with his tenure review talk in CCB at UNM, and is officially up for tenure this year!! Go, Lobos!!! Apology to all graduate students for dropping the ball on our ongoing manuscripts! Thank Emily for the great photo!!!


2023-10-20 The 2023 Science for Health of Indigenous Populations (SHIP) Awardee, Amy, presented her PICK1 research at the SHIP Symposium. 


2023-09-15 Tongtong, Shenghan, and Emily delivered outstanding presentations of their research at the 2023 ACS RMRM in Laramie, WY. Additionally, Dr. He had the honor of serving as co-chair for the Biochemistry session for the first time. It was a valuable experience for everyone!!!! Dr. He also finished the famous Medicine Bow Peak Loop at 12,000 ft within 6 hours with sunburns :-).

2023-09-01 Congratulations to Tongtong and Shenghan whose manuscript titled "Exploring Computational Tools for Improved Structural Design and Stability of Helical AApeptides" has been published by Supramolecular Materials

2023-08-10 Congratulations to Catriona and Emily whose manuscript titled "AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes" has been published by Biomolecules

2023-05-26 We were thrilled to welcome students from East Mountain High School and to share our PICK1 research through the lens of virtual reality. A heartfelt thanks to Cari for organizing this event, to the teachers at EMHS for leading this effort, and to our graduate students for help. I look forward to seeing some of the kids joining our summer research program.


2023-05-25 Congratulations to Tongtong whose manuscript titled "Key factors regulating the inter-domain dynamics may contribute to the assembly of ASC" has been accepted by Biology

2023-05-08 Congratulations to Shenghan whose manuscript titled "Investigating the mechanical properties and flexibility of N-BAR domains in PICK1 by molecular dynamics simulations" has been accepted by Current Protein & Peptide Science

2023-05-08 Congratulations to Emily for her excellent collaborative work with Prof. Vojo Deretic, which has been accepted by the EMBO Journal.

2023-05-05 We were delighted to be invited to visit Miyamura High School in Gallup to present our PICK1 research and its association with substance use disorders. Everyone enjoyed constructing small molecules using virtual reality. Love this photo with the group of brilliant kids!


2023-05-04 Congratulations to Amy who was selected as the 2023 Science for Health of Indigenous Populations (SHIP) Award winner.

2023-04-15 Congratulations to our team from the New Mexico Military Institute (NMMI) for achieving 1st place in the environmental science category and 3rd place overall at the International Science and Engineering Fair (ISEF) qualifying competition in the state of New Mexico. Wishing you the best of luck in Dallas!


2023-03-30 Congratulations to Dr. Yi He who received the NSF Faculty Early Career Development Program (CAREER) Award.

2023-03-29 Congratulations to Emily who received the 2023 NSF-GRFP fellowship. We will officially have two NSF-GRFP Awardees in the house.

2023-03-29 Congratulations to Tongtong and Shenghan who received the Doctoral Conference Presentation Award and Student Research Grant (SRG)

2023-03-02 Congratulations to Tongtong whose cover art design has been selected by The Journal of Physical Chemistry B. This is the FIRST journal cover in He Lab!


2023-02-28 Congratulations to Dr. Yi He who received the SNL University Partnership Network Collaboration-Building Seed Funding.

2023-02-20 Congratulations to Dr. Yi He who received the NIH-funded Regional Alliance of INBRE Networks (RAIN) Award.

2023-02-15 Congratulations to Tongtong AND Emily whose manuscript titled "Simple and effective conformational sampling strategy for intrinsically disordered proteins using UNRES web server" has been accepted by The Journal of Physical Chemistry B

2023-01-16 Please note this opportunity. You can choose to work in any of the C-GEM-associated groups. Welcome to join Walker lab and He lab.


2022-12-02 Super happy to show a group of high school students from northern New Mexico how we use computational tools to explore drug/protein interaction in the Virtual Reality world and also on the huge screen in our Visualization Lab. Had to do Jurassic Park in VR too :-)


2022-11-19 The most powerful GPU, RTX 4090, in the house!!! Our 40-GPU group cluster consists of many different GPUs, such as RTX 4090, RTX 3090 Ti, RTX 3080 Ti, and so on. If you are interested in exploring what you can do with them, welcome to join us! No computational experience is required!


2022-10-11 Congratulations to Amy and John whose manuscript titled "Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations" has been accepted by Protein Science

2022-10-05 Excited to see that the first computational experiment we designed for CHEM 1225L has taken off. Look at the beautiful PICK1 PDZ domain on the screen :-). We hope to bring more computational elements into our curriculum. 


2022-09-29 For the second time we are on UNM News! See it at https://news.unm.edu/news/unm-professors-earn-funding-for-chemistry-student-retention-program

2022-09-19 Congratulations to Emily whose manuscript titled "Insight into the initial stages of the folding process in Onconase revealed by UNRES" has been accepted by The Journal of Physical Chemistry B

2022-08-29 Congratulations to our ROSE scholar Peter whose presentation was selected by New Mexico Science Teachers Association (NMSTA).

2022-08-04 Congratulations to Amy whose manuscript titled "Three binding conformations of BIO124 in the pocket of the PICK1 PDZ domain" has been accepted by Cells

2022-07-15 Congratulations to Tongtong, Stefano, Ale, and the rest of the group whose manuscript titled "Recognizing the binding pattern and dissociation pathways of p300 Taz2 - p53 TAD2 complex" has been accepted by JACS Au

2022-07-12 Congratulations to Amy whose manuscript titled "Benchmarking the accuracy of AlphaFold 2 in loop structure prediction" has been accepted by Biomolecules

2022-06-24 Congratulations to Dr. Mark Walker (PI, visit Mark's group website here) and Dr. Yi He (Co-PI)  who received the NSF Partnerships for Research and Education in Chemistry (PREC) Track 1 Award.

2021-06-05 Welcome our 2022 ROSE scholars Ms. Vania Meetze and Mr. Petervon Tanedo

2022-02-28 Congratulations to our recent work titled "AlphaFold Models Illuminate Half of Dark Human Proteins" which has been accepted by the Current Opinion in Structural Biology

2022-01-27 Congratulations to Dr. Yi He who received the Autophagy, Inflammation, and Metabolism Center Core Capability Enhancement Award.

2022-01-25 Congratulations to Amy whose manuscript titled "Allosterism in the PDZ family" has been accepted by the International Journal of Molecular Sciences

2021-10-20 Still excited after the 2021 NM Science Fiesta at the Explora Science Museum. This is our first in-person Science, Technology, Engineering, Art, and Mathematics (STEAM) in Virtual Reality (VR) outreach in two years. We cannot wait to reach out to other parts of New Mexico! Big shout out to Amy and Emily! We would also like to thank the director of UNM Grand Challenges, Anita, for all her support!  

2021-09-30 Welcome Yujue to our group.

2021-09-03 Congratulations to the He group who received their first NSF grant. The whole group has been working very hard over the summer. Great job!!!

2021-06-25 Four weeks just fly by. We look forward to visiting our ROSE scholars at their school. See you in the Fall, Demvia and Gezi.


2021-06-02 Welcome our ROSE scholars Ms. Demvia Maslian (New Mexico Military Institute, Roswell) and Ms. Gezi Dejka (San Juan College High School, Farmington). 

2021-03-24 Congratulations to Amy who received the 2021 NSF-GRFP fellowship

2020-12-20 Congratulations to Amy whose manuscript titled "Residue-level contact reveals modular domain interactions of PICK1 are driven by both electrostatic and hydrophobic forces" has been accepted by Frontiers in Molecular Biosciences

2020-12-07 Congratulations to Tongtong and Amy who have passed the RP exam. Keep going!

2020-11-16 Congratulations to Amy who received the Smith/Dow Award for 2020. Detailed news can be found at http://chemistry.unm.edu/news-events/news/smith-dow-award-2020.html

2020-09-01 Our research was highlighted in the Grand Challenges Welcome Back Event.sud.png

2020-06-05 Article about our research by Sarah made to the front page of UNM News! Incredible! (Full article can be found at https://news.unm.edu/news/unm-professor-uses-computational-simulations-to-advance-substance-use-disorder-treatment)

2020-06-03 Laura was accepted into the graduate program at Virginia Tech. Congratulations! We will always miss you! 

2020-05-13 Thanks to Sarah for the news report on our PICK1 research at the  UNM Center for Advanced Research Computing (Full article can be found at http://carc.unm.edu/research/professor-simulates-substance-use-disorder-treatment.html)

2020-04-04 Congratulations to Tongtong, Amy, and Laura whose manuscript titled "Changes in structure and flexibility of p53 TAD2 upon binding to p300 Taz2" has been accepted by J. Theor. Comput. Chem.

2020-03-08 Congratulations to Dr. Yi He who received the Research Allocations Committee (RAC) Award.

2020-01-06 Congratulations to Dr. Yi He who was nominated by the University of New Mexico for the ORAU Ralph E. Powe Junior Faculty Enhancement Awards

2019-12-25 Congratulations to Laura and Laurie whose first manuscript titled "Performance of CHARMM36m with modified water model in simulating intrinsically disordered proteins: A case study" has been accepted by Biophysics Reports.

2019-11-15 Finally, we made it. Successfully hosted two workshops of using VR to enhance chemistry education for local high school students. Thank you all for helping to organize these workshops. 

2019-10-24 Thanks to everybody who organizes the Virtual Reality (VR) in Chemistry workshop.

2019-08-22 OMG - We will get access to the fastest supercomputer in the world - SUMMIT at Oak Ridge National Lab. About 1.5 times faster than the second-fastest supercomputer. 

2019-08-16 Yi received the Substance Use Disorders Grand Challenge Pilot Research Award.

2019-08-01 First manuscript submitted! Three more on the way!! go go go!!!!! 

2019-05-15 Jazzel received AMP scholarship.

2019-05-15 David received AMP scholarship.

2019-04-05 Congratulations to Dr. Yi He whose proposal was nominated by the University of New Mexico for the USDA NIFA HSI Education Grants Program.

2019-03-01 Welcome Jazzel and Laurie to our group.

2019-01-25 Congratulations to Dr. Yi He whose proposal was nominated by the University of New Mexico for the Moore Inventor Fellows Award by the Gordon and Betty Moore Foundation.

2019-01-10 Welcome Laura to our group

2018-12-03 Welcome David to our group.

2018-10-01 Welcome Christabel to our group.