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, Ph.D.

Post-doc (joint with the Ward Lab)

Former international graduate student from Mongolia studying structural biology at TSRI. Background in cryo-electron microscopy and virtual screening of membrane proteins. Current project focuses on virtual screening for various membrane proteins (OTOP1, STING) to discover cool molecules. Lightly dabbles in molecular dynamics.

Still loves pineapple on pizza. #pineapple4lyfe

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.

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.

Pietro Scio’

Visiting Ph.D. Student

PhD student from Rome with a Master’s degree in Pharmaceutical Chemistry and Technology. He’s currently developing machine learning based approaches to automatically design small-molecule inhibitors using the predicted thermodynamic properties of structural water molecules. The secret goal of his research efforts is to merge punk rock music with computer-aided drug design.

Peter Rory Hall

Graduate Student (co-mentored with the Ward lab and the Parker lab)

Peter Rory is a Skaggs-Oxford Scholar from England with a background in Ion Channel Biophysics. Currently his research focuses on membrane protein virtual screening and Cryo-EM structural biology. He enjoys marathon running and surfing.

Alessandra Riccio

Post-Doc

Alessandra is a biotechnologist who embraced the nerdy side of science, earning her Ph.D. in Computational Sciences. During her doctoral studies, she combined in-silico modeling with hands-on biophysics to uncover new modulators of immune checkpoint targets, sharpening her expertise in immunotherapy and protein-protein interactions. Now at the Forli Lab, she’s working on developing HIV inhibitors while waving the banner of physical chemistry, convinced that entropy explains everything (yes, including why you can’t stuff toothpaste back into the tube). Despite her love for swimming and dreams of mastering surfing, Alessandra harbors an irrational fear of fish, because, honestly, why do they always look like they know something we don’t? She navigates the complexities of molecular dynamics by day and the intricacies of chord progressions by night.

Joani Mato, Ph.D.

Research Programmer

Theoretical chemist trained in electronic structure theory with focus on excited state and multi reference methods. Joani obtained his PhD from Iowa State University and has been one of the developers of the GAMESS software. Now working on the AutoDock suite of programs, slowly getting used to the world of biology. Always thought Game of Thrones was overrated and air-fryers are just pitiable little ovens.

Lorenzo Angiolini

Visiting Ph.D. Student

A curious and passionate student with a background in Chemical and Pharmaceutical Sciences. During his PhD, he delved into the fascinating world of antibody-drug conjugates (ADCs), mastering various conjugation strategies and characterization techniques to enhance targeted drug delivery. However, scientific curiosity knows no bounds! Trading the lab coat for a keyboard, he now explores how molecules interact in silico using computational tools. And, of course, no pineapple on pizza!

Past Members

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.

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).