Members

Current Members

Stefano Forli, Ph.D.

Associate Professor

M.S. Medicinal Chemistry and Pharmaceutical Technology, Università degli Studi di Siena

Ph.D. Pharmaceutical Sciences, Università degli Studi di Siena

Diogo Santos-Martins, Ph.D.

Senior Staff Scientist

Computational chemist working on the development of force fields and search algorithms for molecular docking to make it more accurate and faster. PhD degree from University of Porto, where he used molecular dynamics, docking and quantum mechanics to study enzymatic mechanisms and molecular recognition in biological contexts.

Writes papers in Vim. Tolerates pineapple on pizza.

Andreas Tillack, Ph.D.

Research Programmer

Statistical Mechanician and Quantum Theoretician with a life-long passion for code development that happens to like organic systems. Diplom-Physics degree from Humboldt-University Berlin (where he built a flow cytometer using a DVD burner), Chemistry PhD from UW, Seattle (where he discovered design rules for organic non-linear optical chromophores by developing an ellipsoidal coarse-grained force field), Post-doc at ORNL speeding up Quantum Monte-Carlo on Summit. He is developing the new generation of AutoDock.

Machine whisperer, mumbles in assembly. The Scotty of our Enterprise. “But captain, I’m givin’ ya all she’s got!”

Matthew Holcomb, Ph.D.

Staff Scientist

Once a graduate student at Scripps Research, he converted from wetlab chemistry to in silico chemistry. Previously worked in the Romesberg Lab on IR spectroscopy in proteins before joining the Forli Lab and dedicating his efforts to the development of libraries of covalent and non-covalent inhibitors.

An organic chemist in a previous life, then saw the Light. Strongly defends the mixing of mint and chocolate.

Chris Garza, Ph.D.

Post-doc

Former graduate of Scripps Research and current member of the UCSD MD-PhD program, with a background in molecular dynamics simulations. His current project studies how the HIV-1 virus disassembles in order to deliver its genetic material to the host cell nucleus. Likes hard problems but won’t admit it. Has offensive taste in chocolate.

Batuujin Burendei

Graduate Student (co-mentored with the Ward Lab)

International graduate student from Mongolia studying structural biology at TSRI. Background in bioscience and cryo-electron microscopy of membrane proteins. While a self-proclaimed “noob” in the ways of computational biology, he is excited to be learning more about research involving molecular docking and virtual screening in the Forli lab.

Loves pineapple on pizza.

Althea Hansel-Harris

Graduate Student (UCSD MD-PhD program)

MD-PhD student studying virtual screening of small molecule inhibitors for applications in cancer. After previously working in both wet-lab cancer biology and anisotropic force field development, she now combines the fields of computational chemistry and cancer biology in the Forli lab.

Strong believer in milk chocolate. Wishes that more Eagles games were broadcast in San Diego.

Niccoló Bruciaferri

Graduate Student

International graduate student from Italy studying new methodologies to improve molecular docking, combining Machine Learning techniques and classical MM/QM calculations. Former bioinformatician with a strong passion for software development and Structural Biology.

Give him headphones and music and he can code for days. Real pasta carbonara lover.

Hung Phan, Ph.D.

Visiting Professor, Soka University of America

Ph.D. Materials Chemistry, University of California Santa Barbara

A scientist and educator bridging the fields of chemistry and computing. His current explorations focus on chemical bonding and ligand-protein interactions using quantum chemistry, molecular docking, molecular dynamics, and machine learning.

Loves pineapple on pizza.

Manuel Llanos, Ph.D.

Post-doc

He obtained his Ph.D. at the National University of La Plata (Argentina), where he combined ligand- and structure-based techniques to find modulators of ion channels and other targets related to epilepsy and neglected diseases. In the lab, he runs mate-fueled MD simulations for drug discovery projects on his MATE-powered workstation.

Likes electronic music and pineapples on cocktails (and mate).

May-Linn Paulsen, Ph.D.

Scientific Associate

Chemical engineer (University of Stavanger, Norway) and oceanographer (Scripps Institution of Oceanography, UCSD), who left physical and analytical chemistry behind to spend more time behind computer monitors. Enjoys automating and abstracting scientific tasks, and making science and software more accessible and user-friendly. A yarn conservative but a pizza-topping liberal.

Johannes Löffler

Post-doc (shared with the Ward Lab)

Computational chemist from Austria working on understanding the role of solvation in drug design and molecular recognition. Graduated from the University of Innsbruck where he developed approaches to quantify binding free energies of small molecules and protein-protein interfaces.

Life motto: No coffee no workee!

Allison Barkdull

Graduate Student

Allison is developing and applying methods to discover molecules which bind to membrane proteins. She received her bachelor’s degree in biomedical engineering from the University of Florida. Allison loves to study proteins embedded in membranes, when she’s not embedded herself in the ocean.

Ishan Taneja

Graduate Student

Skilled coder developing machine learning methods to probe conformational heterogeneity of proteins. Background in computer science. Feels slightly less intimidated by biology than when he began graduate school.

Requires tea and the “right” song to be played on repeat all day in order to code. Strongly believes beard density is the only thing holding him back from becoming a Zen master.

Renhao Luo

Graduate Student (co-mentored with the Patapoutian Lab)

Renhao is working on translational projects to identify potential druggable targets for diseases. He received his Bachelor’s degree in Biological Sciences from the University of California, Irvine, and his Master’s degree in Biomedical Informatics from Harvard Medical School. He is a foodie and enjoys watching movies and relaxing on the beach in his spare time.

Yuting Zhang

Graduate Student (co-mentored with the Kelly Lab)

Obtained her Bachelor’s degree in biology from the University of California, San Diego, and her Master’s degree in translational neuroscience from the University of Oxford. Currently working on applying molecular dynamics and docking to drug discovery in neurodegenerative diseases. Takes an interest in the art of storytelling. Accepts various pizza toppings, including pineapple.

Daniel Del Hoyo Gomez

Graduate Student

PhD student from Madrid, with a bachelor in biotechnology and Master in artificial intelligence. Working in the development of a virtual drug screening platform and related software. Accepts pineapple in pizza, but prefers other toppings. Loves coding, but it’s often not reciprocal.

Amy He, Ph.D.

Post-doc

B.S. Chemistry, Zhejiang University

Ph.D. Chemistry, Ohio State University, Columbus, Ohio

Born and raised on the lakeside of Shicheng, Zhejiang, China. Avid gamer, long-time fan for game jikkyo, loves to travel with books and Toblerone.

Past Members

Parnika Sharma

Research Programmer III

A software developer with an appreciation for chemistry, she is excited to be working with scientists again to develop tools and user interfaces the Forli lab. She has experience working with ML models, XR development, and game development. Loves the performing arts, tea, and chocolate of all kinds.

Paolo Governa, Ph.D.

Post-doc

Pharmaceutical chemist with background in natural products. He is involved in the identification and development of active compounds through in silico structure- and ligand-based virtual screening. Loves heavy metal and stylish Vim color schemes. No pineapple on pizza.

Giulia Bianco, Ph.D.

Post-doc

She did her PhD in Cagliari, where she mainly focused on structure-based approaches on pharmaceutical relevant targets. She is part of the HIVE center, where she aims at finding potential inhibitors of the viral assembly of HIV-1. She is also involved in the development of new covalent docking methods with the Software AutoDock.

If it’s covalent, she knows about it. Very patient with pineapple.

Jérome Eberhardt, Ph.D.

Post-doc

Master of waterbending, involved in the development of a new desolvation model for the AutoDock docking software. He obtained his PhD diploma at the University of Strasbourg (France), where he worked on nuclear receptors and the interpretation of experimental data (Hydrogen/Deuterium eXchange, NMR) using enhanced molecular dynamic simulation methods. His motto: “With the right tool every wall can be a door”.

Despite his leader’s disapproval, he is also a fervent supporter of the carbonara sauce with cream (can kill a carbonara in 19 more ways).