People
David Mobley (Principal Investigator)
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 -
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.
Post-Doctoral Researchers
Swapnil Wagle -
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.
Alžbeta Kubincová -
Alžbeta graduated in Chemistry from ETH Zürich in Switzerland, and obtained her Ph.D. at the same institution in the group of Prof. Philippe Hünenberger, working on adaptive-resolution simulations and force-field development and parameterization. In 2021, she moved to Exscientia in the UK to work on active learning workflows for relative binding free energy calculations. After a brief stint in a software engineering role back in Switzerland, she joined Mobley Lab in 2024 to work on active learning approaches to inform the construction of DNA-encoded libraries.
Graduate Students
Martin Amezcua (Pharmaceutical Sciences) -
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.
Trevor Gokey (Chemistry) (Joint with Ioan Andricioaei) -
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.
Ana Caldaruse (Pharmaceutical Sciences) -
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) -
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.
Meghan Osato (Pharmaceutical Sciences) -
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.
Undergraduate Students
Melissa Plata (Pharmaceutical Sciences)
Evien Cheng (Pharmaceutical Sciences)
Alumni
| Name | Tenure 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. Suleyman Selim | Postdoc (2023-2024) | Assistant Professor, Ege University |
| 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 |
| Dr. Chris Zhang | Graduate Student (2018-2024) | Data Scientist at Meta |
| Dr. Anjali Dixit | Graduate Student Joint with Dr. Brian Paegel (2019-2024) | TBA |
| 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 (2023) | Masters student from University of Leiden |
| Linde Schoenmaker | Visiting Scholar (2023-2024) | PhD student from University of Leiden |
| Fabian Sendzik | Visiting Scholar (2024) | PhD student from University of Dortmund |
| 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. |
| James Hariyanto | Undergraduate student | PharmD student, Western University |
| Linh Nguyen | Undergraduate student | Finished her B.S. degree in Pharmaceutical Sciences and is now a PharmD student, Chapman University |
| Meghan Osato | Undergraduate student | Finished her B.S. degree in Pharmaceutical Sciences and is now a PhD Student, Pharmacological Sciences UCI |
| Amanda Nguyen | Undergraduate student | Finished her B.S. degree in Pharmaceutical Sciences and is now a PhD student, Pharmacological Sciences UCI |
| Byron Tjanaka | Undergraduate student | TBA |
| Jordan Ehrman | Undergraduate student | Ph.D. student, University of Washington |
| Mel Bedolla Loaiza | Undergraduate student | TBA |
| Jennifer Huang | Undergraduate student | Finished her B.S. degree in Pharmaceutical Sciences |