People

David Mobley (Principal Investigator)

dmobley

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.



Scientists

Pavan Behara -

pbehara

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

Post-Doctoral Researchers

Swapnil Wagle -

swagle

Swapnil received his M.Sc. Integrated degree in Chemistry from IIT Kanpur, India, in 2015. After graduation, he moved to Germany for his Ph.D. in Computational Biophysics at the Max Planck Institute for Colloids and Interfaces, Potsdam, working on enhanced sampling free-energy calculations on protein-membrane systems. Thereafter, he joined Prof. Heather Carlson’s lab at University of Michigan as a postdoc in 2020, working on chemical similarity calculations of ligands and training machine learning models for protein binding sites similarity calculations. Swapnil joined Mobley Lab in 2022 as a postdoctoral fellow, to work on developing effective approaches for alchemical binding free-energy calculations of protein-ligand systems with buried water molecules. Swapnil aspires to become a successful computational chemist with expertise in machine learning, to accelerate modern day drug-discovery research.

LinkedIn



Suleyman Selim -



Graduate Students

Martin Amezcua (Pharmaceutical Sciences) -

amezcum1

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) -

chrisz1

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



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

tgokey

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) -

dixitaa

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) -

acaldaru

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 testing ring breaking and formation using the Separated Topologies approach which cannot be handled by traditional relative binding free energy approaches. Being able to handle ligands with diverse scaffolds will broaden the scope of applicability of binding free energy approaches 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) -

anandkeo

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 in the 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 properties.

LinkedIn



Meghan Osato (Pharmaceutical Sciences) -

mosato

Meghan Osato graduated from UCI with a B.S. in Biological Sciences and a B.S. in 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. Meghan was previously a technician in the Mobley Lab working on containerized methods for the SAMPL Challenges. Currently, she is a graduate student in the lab working on binding free energy calculations.

LinkedIn



Undergraduate Students

Melissa Plata (Pharmaceutical Sciences)

Evien Cheng (Pharmaceutical Sciences)

Jennifer Huang (Pharmaceutical Sciences)

Alumni

Name Tensure in the Lab Current Position
Dr. Jeff Wagner Staff Scientist (2018-2020) OMSF Consortium
Dr. Adam Van Wart Postdoc (2015) Adjunct chemistry professor at several community colleges in Orange County, California.
Dr. Sreeja Parameswaran Postdoc Senior Analyst in Bioinformatics, 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. 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. Sukanya Sasmal Postdoc (2017-2019) pharma; molecular modeling
Dr. Lea El Khoury Postdoc (2017-2021) Team Leader in Molecular Modeling at Qubit Pharmaceuticals
Dr. Yunhui Ge Postdoc (2020-2022) Scientist at Alkermes
Dr. Mary Pitman Postdoc (2021-2023) Scientist at Sandbox AQ
Dr. 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.
Dr. Shuai Liu Graduate Student (2010-2015) Drug discovery with XtalPi in the Boston area.
Dr. Camilla Zenette Graduate Student (2013-2019) Bioinformatician, Agendia in the Irvine area
Dr. 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.
Dr. Nathan Lim Graduate Student (2014-2019) Scientist, Janssen Pharmaceuticals in San Diego
Dr. Kalistyn Burley Graduate Student (2015-2020) Applications Scientist at OpenEye, Cadence Molecular Sciences
Dr. Caitlin Bannan Graduate Student (2014-2019) Applications Scientist, OpenEye Scientific Software Inc. Developing methods for crystal structure prediction using machine learning.
Dr. Sam Gill Graduate Student (2014-2020) Ventus Pharma, molecular modeling.
Dr. Victoria Lim Graduate Student (2015-2020) Senior Technical Writer, Imply
Dr. David Wych Graduate Student (2016-2021) Scientific Developer II — cryoEM — OpenEye Scientific, Cadence Molecular Sciences
Jessica Maat Graduate Student (2017-2022) TBA
Dr. T. Danielle Bergazin Graduate Student (2017-2022) Senior Cheminformatics Engineer, Booz Allen Hamilton
Oanh Tran Graduate Student (2018-2023) Harmonic Discovery Cheminformatics Intern
Dr. Hannah Baumann Graduate Student (2018-2023) Postdoc at OpenFreeEnergy
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.
Lily Wang Fullbright Visiting Scholar (2021) Science Lead, Open Force Field Initiative
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 Application Scientist, Chemical Computing Group.
Daan Jiskoot Visiting Scholar Masters student from University of Leiden
Linde Schoenmaker Visiting Scholar PhD student from University of Leiden
Mel Bedolla Loaiza Undergraduate student TBA
Jordan Ehrman Undergraduate student Ph.D. student, University of Washington
Byron Tjanaka Undergraduate student TBA
Amanda Nguyen Undergraduate student PhD student, Pharmacological Sciences UCI
Linh Nguyen Undergraduate student PharmD student, Chapman University
James Hariyanto Undergraduate student PharmD student, Western University
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.