Sorin Lab News

2019 Updates (see archive)

news photo Chemistry MS graduate Parker Bremer has been accepted into the Chemistry PhD program at UC Davis!

news photo CAMS high schooler and Sorin Labber Joceyln Hsu entered the Biomedical Engineering program @ Johns Hopkins University

news photo Chemical Engineering major Nguyet Nguyen received a Women & Philanthropy Scholarship to support her research!

news photo Chemistry major Danna De Boer co-authored her first article, which she'll present at the 2020 Biophysical Society annual meeting in Feb!


2018 Updates (see archive)

news photo Sorin Lab veteran Walter Alvarado completed his Physics MS Thesis and entered the Biophysics PhD program at the University of Chicago

news photo Nick Humphrey completed his BS in Chemical Engineering in spring and entered the Materials Science PhD program at USC this fall

news photo RISE Fellow Xavier Martinez completed his BS in Computer Science this spring and is now a professional web developer at JURISTERRA


2017 Updates (see archive)

news photo Sorin Lab alumnus/B.S. Biochemistry graduate Dakota Rochelle begins his dental training this fall in the D.D.S. program @ UCSF

news photo Recent Biochem/Physics graduate Yessica Gomez received the 2017 Hypercube Award and begins her Ph.D. in Biophysics this fall @ UCSF

news photo M.S. Computer Science major Vardo Barsegyan earned an Engineering Alumni Scholarship and a CSULB Summer Research Award


Computational Biochemistry & Biophysics

Members of the Sorin Lab study the structure and dynamics of biological molecules via computer modeling and simulation. Using cluster computing and the Folding@Home Distributed Computing Project, we can apply a variety of models and methods to sample large numbers of independent simulations: we are now capable of simulating some molecular events in dynamic equilibrium, making simulation a powerful tool with which to probe topics in molecular biology and biophysics including molecular recognition and drug design, RNA and protein folding, and related processes. [ Click here to apply for a position (.doc application) ]

Sorin Lab June 2012

Prof. Eric J. Sorin, Mariell Abad, Jia Mao, Nguyet Nguyen,
Aingty Eung, Trevor Chapman, Jocelyn Hsu, Parker Bremer, Jake Bremer,
Angela Choy, Justin Mubatas, and Danna De Boer


Recent Publications

JCIM
Overcoming the Heuristic Nature of k-means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes. Parker Ladd Bremer, Danna De Boer, Walter Alvarado, Xavier Martinez, & Eric J. Sorin* (2020). Journal of Chemical Information and Modeling, DOI:10.1021/acs.jcim.9b01137.

Understanding the Enzyme-Ligand Complex: Insights from All-Atom Simulations of Butyrylcholinesterase Inhibition. Walter Alvarado, Parker Ladd Bremer, Angela Choy, Helen N. Dinh, Aingty Eung, Jeannette Gonzalez, Phillippe Ly, Trina Tran, Kensaku Nakayama*, Jason P. Schwans*, and Eric J. Sorin* (2019). Journal of Biomolecular Structure & Dynamics, 38(4), doi:DOI:10.1080/07391102.2019.1596836.

Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcho linesterase inhibitors. Kensaku Nakayamaa*, Jason P. Schwans*, Eric J. Sorin*, Trina Tran, Jeannette Gonzalez, Elvis Arteaga, Sean McCoy & Walter Alvarado (2017). Bioorganic & Medicinal Chemistry, 25(12), 3171–3181, doi:10.1016/j.bmc.2017.04.002.

ApoE
Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot . Khai K. Q. Nguyen, Yessica K. Gomez, Mona Bakhom, Amethyst Radcliffe, Phuc La, Dakota Rochelle, Ji Won Lee & Eric J. Sorin* (2017). Nucleic Acids Research 45, doi:10.1093/nar/gkx012.

ApoE
Ensemble Molecular Dynamics of a Protein-Ligand Complex: Residual Inhibitor Entropy Enhances Drug Potency in Butyrylcholinesterase. Eric J Sorin*, Walter Alvarado, Samantha Cao, Amethyst Radcliffe, Phuc La & Yi An (2017). Bioenergetics 6(1), DOI:10.4172/2167-7662.1000145.