People

David Mobley (Principal Investigator)

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David Mobley did his undergraduate work in Physics at the University of California, Davis, graduating in 2000. After that he finished a M.S. (2002) and a Ph.D. (2004) in Physics at UCD, doing graduate research in condensed matter theory and biophysics with Daniel L. Cox and Rajiv Singh. Following his Ph.D. he took a position with Ken Dill at the University of California, San Francisco, doing molecular simulations relating to protein-ligand binding and hydration thermodynamics. This work ultimately moved with him to the University of New Orleans. However, after his postdoc ended in 2008, he did a brief stint as Chief Science Officer of a startup company (Simprota Corporation) doing contract work designing peptide diagnostics. He then left to join UNO in Fall 2008. Then, in 2012, after almost 4 years at UNO, he moved to his current position in Pharmaceutical Sciences at the University of California, Irvine. In January 2013 he also received a joint appointment in the Department of Chemistry at UCI. He was promoted to Associate Professor at UCI, and received tenure, in July 2014, then was promoted to Professor in 2018. He served on the advisory board for Schrodinger software from 2013-2016. He currently serves on the editorial boards of the Journal of Computer-Aided Molecular Design and the Journal of Molecular Recognition, on the scientific advisory board for OpenEye Scientific Software, as a founding and managing editor for the Living Journal of Computational Molecular Science, and as an Open Science Fellow for Silicon Therapeutics. He also maintains a personal blog where he writes about his Christian faith and other issues.

Post-Doctoral Researchers

Yunhui Ge -

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Yunhui Ge pursued his PhD study in computational chemistry in Dr. Vincent Voelz lab at Temple University in Philadelphia. After he graduated in 2020, he joined the Mobley lab in UC Irvine as a postdoc. His research has been focused on (1) exploring enhanced sampling techniques for water molecules and their applications in binding free energy calculations; (2) using molecular dynamics simulations and docking algorithms for virtual screening and lead optimization; (3) applying Markov state model approaches to investigate folding and binding mechanisms for different systems; (4) developing a Bayesian inference approach to reconcile experimental measurements with simulations predictions for structural determination and model selection.

LinkedIn - Google Scholar

Pavan Behara -

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Pavan Behara graduated in Chemical Engineering from Birla Institute of Technology and Science, Pilani in 2011. He worked for a year in the R&D division of Aditya Birla Group on Alumina refining processes. In 2012, he moved to University at Buffalo, SUNY, for a Masters degree and worked on understanding demixing phenomenon in binary hardsphere mixtures. He started his PhD research in 2015 on modeling charge carrier dynamics in renewable energy materials using Ab initio quantum chemistry methods. Pavan joined Mobley Lab, under Openforcefield initiative in Sep 2020, to work on development of small molecule force fields for pharmaceutically relevant chemical space.

LinkedIn

Mary Pitman -

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Dr. Mary Pitman is a postdoc in the Mobley lab with a habit of reimagining biological phenomena through the lens of theory. She did her doctoral research in the Papoian lab at the University of Maryland and as a Fellow for Integrative Cancer Research at NCI/NIH. Mary aspires to lead a brigade of curious individuals to improve patient outcomes.

Github - Researchgate - LinkedIn - ORCiD




Graduate Students

Jessica Maat (Chemistry) -

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Jessica joined the Mobley group in 2018. She graduated University of Massachusetts Amherst in 2017 with a B.S. in Applied Mathematics and Chemistry. She worked with Prof. Christine Isborn from UC Merced on her undergraduate honors thesis on calculating the hyperpolarizaibility of organic electrooptic chromophores and modeling their excited state coupling. Jessica currently works on improving accuracy of force fields in the Open Force Field Initiative. Specifically her project focuses on developing using data driven methods to improve energetics and geometries of trivalent nitrogens, a very prevalent chemical feature in small drug molecules.

Danielle Bergazin (Pharmaceutical Sciences) -

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Danielle joined the Mobley lab in 2018 under the Pharmacological Sciences Ph.D. program. Her previous work involved contributing to the development and application of BLUES, and is currently involved in the SAMPL series of blind challenges. Her long-term research interest is to produce computational methods that reduce the cost of drug discovery, as well as expand the applications of computational chemistry in drug discovery.

Hannah Baumann (Pharmaceutical Sciences) -

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Hannah graduated from Johannes-Gutenberg University Mainz, Germany, with a pharmacy degree in 2018. During her time in pharmacy school she worked with Prof. González at the University Jaume in Castelló de la Plana, Spain, synthesizing a new cysteine protease inhibitor against Trypanosoma. She also did an internship for six months at Merck KGaA, Darmstadt, where she applied relative binding free energy calculations in ongoing drug discovery projects. Motivated by this experience, Hannah decided to come to UC Irvine, where she joined the Mobley lab in Fall 2018. Her research focuses on developing an alternate approach for relative binding free energy calculations, Separated Topologies. Hannah’s main interest is to develop and improve computational methods that help discover new drugs.

LinkedIn

Martin Amezcua (Pharmaceutical Sciences) -

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Martin Amezcua graduated from CSUF with a B.S. in Biochemistry. During this time, under the tutelage of Dr. Nicholas Salzameda, his research work involved computational modeling and docking, synthesis, and evaluation of dipeptide small molecules as potential counter measures against Botulinum Neurotoxin-A. He entered UCI’s Pharmaceutical Sciences PhD program in 2018, where he joined the Mobley Lab. His current work is primarily on the SAMPL (Statistical Assessment of the Modeling of Proteins and Ligands) challenges to test and study computational methods and tools for predicting binding thermodynamics of host-guest systems to help improve their accuracy for computer aided drug design.

Chris Zhang (Chemistry) -

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Chris Zhang graduated from Harvard University with a Bachelors in Chemistry. During his undergrad, he worked in Alan Aspuru-Guzik’s lab applying machine learning methods to chemistry. He is currently developing computational tools to analyze DNA-encoded libraries.

LinkedIn




Oanh Tran (Chemistry) (Joint with Thomas Poulos) -

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Oanh Tran completed her B.S. and B.S.A. at the University of Texas at Austin in biochemistry and chemistry. As an undergraduate student, Tran worked on multiple research projects from her institution as well as from other internships across the U.S. She is currently pursuing a Ph.D. and working in both the Mobley lab and the Poulos lab. She also has the best corgi in the world, named Brisket.

LinkedIn



Trevor Gokey (Chemistry) (Joint with Ioan Andricioaei) -

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Trevor Gokey earned an MS in Computer Science at San Francisco State University and a BA in Psychology from CSU Long Beach. He works with OpenFF to design force fields, where he focuses on efficient ways to encode and search chemical space. His interests are at the intersection of high performance computing and multiscale modeling. Outside of research, Trevor enjoys roasting coffee and perfecting espresso, building clusters, and pipe organs.


Anjali Dixit (Pharmaceutical Sciences) (Joint with Brian Paegel) -

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Anjali Dixit is a Pharmaceutical Sciences Ph.D. student who is co-advised by Dr. David Mobley and Dr. Paegel. She graduated from the University of California Santa Barbara with BS in pharmacology and BA in psychology. In her undergraduate career, Anjali’s research centered around neuroimaging and decision-making research. In her graduate career, her project aims to strengthen the role of cheminformatic involvement in DNA-encoded library combinatorial synthesis and library design. Using machine learning tools, she hopes to inform future generations of library development towards rationally designed chemical space

LinkedIn - ORCiD

Ana Caldaruse (Pharmaceutical Sciences) -

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Ana graduated with her B.S. in Biochemistry and Molecular Biology from UC Santa Cruz in 2015. She did research in undergrad but didn’t feel ready for a PhD after graduation so she sought out research positions before applying to graduate school. She worked for a clinical trials company and in research at Cedars Sinai Medical Center where she studied the molecular mechanisms of heart failure and development of a blood based bioassay to determine disease progression. In 2020, Ana made the transition into the Pharmacological Sciences PhD program at UC Irvine and joined the Mobley lab. Her work focuses on implementing separated topologies approach into the Lead Optimization Mapper (LOMap) to plan out binding free energy calculations that can be used in the pharmaceutical industry. Besides research she likes to be involved in mentoring students to help ease their transition into graduate school. Other things that bring Ana joy are reading – particularly dystopian novels, trying new coffee shops, and experiencing new cultures through travel and cuisine.

UCI email - GitHub - LinkedIn - ORCiD

Aakankschit Nandkeolyar (Pharmaceutical Sciences) -

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Aakankschit (AK) Nandkeolyar graduated with a B.S. and M.S. in Biomedical Engineering from Drexel University in Philadelphia. He completed an internship with the automation team at GLaxoSmithkline (GSK) where he found an interest for pharmaceutical sciences. AK worked on curating a dataset of physical properties for the blind challenge series SAMPL (Statistical Assessment of Modeling of Proteins and Ligands). AK continued his collaboration with GSK through his graduate research at Drexel, which focused on building machine learning models to predict clinical outcomes in patients based on data obtained from quantitative systems pharmacology models. At the Mobley Lab, he continues to work on the SAMPL project evaluating different modeling methods for accuracy in predicting physical proterties.

LinkedIn

Megan Osato (Pharmaceutical Sciences) -

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Meghan Osato graduated from UCI in 2020 with Bachelor’s degrees in Biological Sciences and Computer Science. During her undergrad, she worked in the Mobley Lab on protein-ligand binding mode prediction using MD and BLUES simulations. Upon graduating she worked with Dr. Antoni Luque at San Diego State University modeling bacteriophage capsid geometry. Currently, Meghan is a technician in the Mobley Lab working on containerized methods for the SAMPL Challenges. She plans to join the Mobley Lab in Fall 2022 as a PhD student.

LinkedIn

Alumni

Name Tensure in the Lab Current Position
Dr. Sukanya Sasmal Postdoc (2017-2019) pharma; molecular modeling
Dr. Gaetano Calabró Postdoc (2017) Scientific software development with OpenEye Scientific Software in Santa Fe. Continues to collaborate with the Mobley Lab on MD-related software development.
Dr. Adam Van Wart Postdoc (2015) Adjunct chemistry professor at several community colleges in Orange County, California.
Dr. Sreeja Parameswaran Postdoc Took time off to raise her family, then started a position in data science as an Application Developer at Cincinatti Children’s Hospital in the Center for Autoimmune Genomics and Etiology.
Dr. Shun Zhu Postdoc Faculty member in the Department of Cellular and Genetic Medicine at Fudan University in China.
Dr. Lea El Khoury Postdoc (2017-2021) Team Leader in Molecular Modeling at Qubit Pharmaceuticals
Pavel Klimovich Graduate Student (2009-2015) Pavel is a man of mystery; he sends us postcards from random parts of the world, but he’s a man of secrecy and we have no idea what he is doing, other than that he is still in science somewhere.
Shuai Liu Graduate Student (2010-2015) Drug discovery with XtalPi in the Boston area.
Camilla Zenette Graduate Student (2013-2019) Bioinformatician, Agendia in the Irvine area
Guilherme D. R. Matos Graduate Student (2013-2019) Postdoc, Prof. Robert C. Rizzo’s group at Stony Brook University in New York. Advancing docking techniques for predicting protein-ligand binding interactions.
Nathan Lim Graduate Student (2014-2019) Postdoctoral Researcher, Janssen Pharmaceuticals in San Diego
Caitlin Bannan Graduate Student (2014-2019) Applications Scientist, OpenEye Scientific Software Inc. Developing methods for crystal structure prediction using machine learning.
Sam Gill Graduate Student (2014-2020) Ventus Pharma, molecular modeling.
Victoria Lim Graduate Student (2015-2020) Technical Writer, Ionis, Patent Area
David Wych Graduate Student (2016-2021) Scientist Los Alamos National Laboratory
Anasuya Kolavennu Masters Student (UNO) She is currently a high school teacher in India
Jessica Fuselier Masters Student (UNO) She is currently pursuing a second M.S. degree in bioinformatics at IUPUI.
Hanh Nguyen Masters Student Obtained a position at a R&D laboratory.
Noora Siddiqui Masters Student Currently working in Baylor College of Medicine as a Programmer Analyst.
Lilly Wang Fullbright Visiting Scholar (2021) PhD Student Australlian National University
Zuzana Jandova Visiting Scholar (2018) From Chris Oostenbrink’s group in Vienna
Max Riquelme Visiting Scholar (2017) From Esteban Vöhringer-Martinez’s group in Chile
Stefania Evoli Visiting Scholar From University of Calabria in Italy. Continued onto a postdoc position with Jeff Wereczsynski at IIT.
Daisy Kyu Undergraduate Student Finished her B.S. degree in Pharmaceutical Sciences and is in pharmacy school at the University of Southern California.
Nam Thi Undergraduate Student Finished his B.S. degree in Pharmaceutical Sciences and is in pharmacy school at Loma Linda University School of Pharmacy.
Kevin Hoang undergraduate Student Finished his B.S. degree in Pharmaceutical Sciences and is pursuing pharmacy school.
Karisa Wymer Undergraduate Student Finished her B.S. degree in Pharmaceutical Sciences at UCI and is attending Pharmacy school at University of California, San Francisco.
Kim Keyes Undergraduate Student (UNO) Chemical analyst at Eurofins in New Orleans.
Vivian Jaber Undergraduate Student (UNO) MD/Ph.D. student at Louisiana State University in New Orleans.
Sheldon Williams Undergraduate Student (UNO) Finished his undergraduate degree at Southern University in New Orleans.
Yu Xuan “Luna” Liu Undergraduate Student (UNO) Graduate student in oriental medicine.
Christopher D. Savoie Undergraduate Student (UNO) Completed his M.S. degree in Chemistry at Boston University with Tom Keyes and is working as a Nuclear Officer for the U.S. Navy.