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Research: OpenPandemics - COVID-19: Research Participants Collapse   Expand  
 

Research Participants

Scripps Research

La Jolla, California, USA

Scripps Research is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in La Jolla, California, with a sister facility in Jupiter, Florida, the institute has 250 laboratories employing 2,400 scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world.

Stefano Forli, PhD

Assistant Professor
Center for Computational Structural Biology
Department of Integrative Structural and Computational Biology
OpenPandemics Principal Investigator

Stefano Forli trained at the Università degli Studi di Siena, Italy, where he graduated in Pharmaceutical Chemistry and Technology in 2002, and obtained his PhD in Pharmaceutical Sciences in 2006. He then joined the Molecular Graphics Laboratory led by Arthur Olson at The Scripps Research Institute in 2008. In 2015, he started his own laboratory at the Center for Computational Structural Biology. The main research interests of his lab are the design of structure-based computational methods for drug discovery and design, and their application on biologically and therapeutically relevant targets. The Forli lab leads the development of the AutoDock Suite.

forlilab.org

Giulia Bianco, PhD

Research Associate
forlilab.org/members/

Giulia Bianco started her postdoc at Scripps Research in 2018 after her PhD in Italy, where she mainly focused on structure-based approaches on pharmaceutical relevant targets. She is part of the HIVE center, where she aims to find potential inhibitors of the viral assembly of HIV-1, and she is also involved in the development of new covalent docking methods with the software AutoDock.

Jérôme Eberhardt, PhD

Research Associate
forlilab.org/members/

Jérôme Eberhardt has been a post-doc at Scripps Research since 2017, and is involved in the development of a new desolvation model for the AutoDock docking software. He obtained his PhD diploma at the University of Strasbourg in France. His main research project was focused on nuclear receptors and the interpretation of experimental data (Hydrogen/Deuterium eXchange, NMR) using enhanced molecular dynamic simulation methods.

Matthew Holcomb

Graduate Student
forlilab.org/members/

Matthew Holcomb is a fifth-year graduate student at Scripps Research who converted from wet lab chemistry to in silico chemistry. He 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 noncovalent inhibitors.

Christina Garza

Graduate Student
vivo.scripps.edu/display/GarzaChristina

Christina Garza is a third year MD-PhD student studying viral biophysics with Drs. Forli and Torbett at Scripps Research. She has a background in molecular dynamics simulation. Her current project aims to study the process of viral maturation and delivery of genetic information to the host cell.

Batuujin Burendei

Rotating Graduate Student
vivo.scripps.edu/individual/BurendeiBatuujin

Batuujin Burendei is an international graduate student from Mongolia, studying structural biology at Scripps Research. His background is 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. In this project, as a part of the Structure Team, he is involved in preparing the protein targets and identifying suitable ligand binding pockets for virtual drug screening.

Paolo Governa

Visiting Ph.D. student

Paolo Governa is a PhD student in Chemical and Pharmaceutical Sciences at the University of Siena, Italy. His main research project involves the study of the bioavailability of natural products from herbal species, by integrating cell biology and computational methods.

Andreas F. Tillack, PhD

Research Programmer

Andreas Tillack is a Statistical Mechanician and a Quantum Theoretician with a life-long passion for code development who happens to like organic systems. He is fluent in German, English (et un peu français), C, C++, Cuda, OpenCL, and many more languages. He holds a Diplom-Physics degree from Humboldt-University Berlin where he built a flow cytometer; and a Chemistry PhD from UW, Seattle developing a coarse-grained ellipsoidal force field. He did Postdoc work at Oak Ridge National Lab on the nation’s largest supercomputer, Summit, speeding up Quantum Monte-Carlo. He is currently a Research Programmer at Scripps Research developing the new generation of AutoDock with a team of outstanding scientists.

Diogo Santos-Martins, PhD

Research Associate

Diogo is a computational chemist working on molecular docking software. His work concentrates on making docking force fields more accurate and to make docking faster. He received a PhD from University of Porto, where he used molecular dynamics, docking and quantum mechanics to study enzymatic mechanisms and molecular recognition in biological contexts. In the OpenPandemics project, his role is to prepare the models of the small molecules for virtual screening.

Martina Maritan, PhD

Research Associate

Martina is a postdoc in the David Goodsell and Arthur Olson laboratories at Scripps Research. She has a background in X-ray crystallography and biophysics for protein characterization. Her current research focuses on developing tools for mesoscale modeling.

 

Collaborators

The collaborators, coordinated by Dr. Forli, provide support for further modeling, experimental characterization of the results, and synthesis and chemical modification of the hits. In particular, the collaborators will test the compounds in biochemical and functional assays, from isolated proteins to more complex settings, including infectivity assays. The structural biology teams will characterize the structure of the virtual screening hits when bound to their target viral proteins.

David Goodsell

Professor of Computational Biology, Scripps Research &
Research Professor, Rutgers State University of New Jersey

David Goodsell's research centers on methods for computational structural biology and their application to drug design, protein function prediction, and modeling of the molecular structure of entire cells. He is currently applying these methods to HIV drug resistance and structure and function of bacterial cells. He is also active in science outreach, including two decades of work on depiction of the cellular mesoscale, and development of non-photorealistic rendering methods for molecular and cellular subjects. He currently creates outreach materials for the RCSB Protein Data Bank, including a popular monthly column that presents molecular structure and function for general audiences.

Ian Wilson

Hansen Professor of Structural Biology
Chairman, Department of Integrative Structural and Computational Biology
Scripps Research, La Jolla, CA

The main focus of the Wilson lab is on immune recognition and on how pathogens are recognized by the adaptive and innate immune systems. Their major goals are to understand the interaction and neutralization of foreign antigens by the immune system through structural studies using mainly high-resolution X-ray crystallography. The information derived from these studies is being used to develop antigens and immunization regiments to elicit broadly neutralizing antibodies against viral pathogens, such as influenza virus and HIV-1.

Philip Dawson

Professor, Department of Chemistry
Dean, Skaggs Graduate School
Scripps Research, La Jolla, CA

Philip Dawson received an A.B. (1992) in Chemistry from Washington University, and Ph.D. (1996) from Scripps Research. After pursuing postdoctoral work at Caltech, he returned to Scripps as an Assistant Professor in 1997. Professor Dawson is a pioneer of chemoselective ligation methods for the synthesis of complex macromolecules including peptides, proteins, glyocproteins and nucleic acids and in the development of constrained bioactive peptides and epitopes. He has applied these tools broadly to understand complex biological systems.

Andrew Ward

Professor of Integrative Structural and Computational Biology
Scripps Research, La Jolla, CA

The Ward lab uses electron microscopy to understand the interface of the immune system and viral pathogens at atomic resolution. We then use these data to design new vaccines or immunotherapeutics.

Stefan Sarafianos

Nahmias-Schinazi Distinguished Professor of Pediatrics
Emory University School of Medicine, Department of Pediatrics, LOBP

The Sarafianos Laboratory works towards unraveling the molecular details of how biomedically-relevant enzymes function, how they are inhibited, how they develop drug resistance and towards developing drugs to treat human disease by novel mechanisms of action. They use conventional and cutting-edge research tools, including virology, protein biochemistry, fluorescence imaging/microscopy, X-ray crystallography, cryo-electron microscopy, molecular modeling, enzymology, and high-throughput technologies. Ongoing efforts focus on various steps of HIV, SARS-CoV-2, Hepatitis B virus HBV, Hepatitis C virus life cycles.

Dennis Wolan

Associate Professor
Department of Molecular Medicine
Scripps Research

The Wolan laboratory focuses on the discovery and design of small molecule and peptide-based modulators of enzymatic activities to gain unprecedented insight into the functional significance of proteins within biological processes. They employ an array of biophysical and cellular methods to identify new and exciting protein targets, improve and develop high-throughput screening technology, validate potential lead molecules, and increase the spatial and temporal resolution of specific enzymatic functions within biological systems.

Patrick Griffin

Professor, Co-chair
Department of Molecular Medicine
Scripps Research

The focus of research of the Griffin lab is on protein structure and function, particularly on mutational- and ligand-mediated alterations in protein structural plasticity, as well as quantitative SAR to facilitate lead optimization of molecules targeting therapeutic proteins. Using mutagenesis, HDX-MS, crystallography, proteomics and genomics, the lab’s research is focused on structure-function of nuclear receptors, enzymes, and G protein coupled receptors (GPCRs). The research program has a major focus on understanding nuclear receptor (NR) signaling using structural, chemical and biological approaches. They have made significant contributions to understanding the mechanism of ligand activation of NRs such as PPARs, RORs, REV-ERBs, LRH1, VDR, ER, GR, and PR.

Bruce Torbett

Associate Professor
Department of Immunology and Microbiology
Scripps Research, La Jolla, CA

The Torbett Laboratory has three research areas: Evolution of HIV-1 inhibitor resistance and fitness; Hematopoietic stem and T cell gene delivery strategies to block HIV-1entry and limit infection; and the regulation of normal and abnormal myeloid development and function by the ets transcription factor PU.1 (spi).

Alan Engelman

Alan Engelman

Professor of Medicine, Harvard Medical School Principal Investigator, Cancer Immunology and Virology, Dana-Farber Cancer Institute

Dr. Engelman focuses on the mechanism of human immunodeficiency virus type 1 (HIV-1) integration, an essential step in the viral lifecycle. Retroviruses encode their own integrase protein, and Dr. Engelman's research borrows from numerous disciplines including molecular virology and structural biology to understand mechanistic details of integrase function. Lentiviruses like HIV-1 preferentially target active genes during integration, and Dr. Engelman`s research established that an interaction between integrase and the cellular chromatin binding protein lens epithelium-derived growth factor (LEDGF) plays a significant role in HIV integration targeting.