The Scripps Research Institute
La Jolla, California, USA
The Scripps Research Institute (TSRI) is a nonprofit research institution whose philosophy emphasizes the creation of basic knowledge in the biosciences for its application in medicine and the pursuit of fundamental scientific advances. The more than 200 principal investigators at TSRI include many distinguished leaders in their fields, including two Nobel laureates and numerous members of the National Academy of Sciences (including its Institute of Medicine), American Academy of Arts and Sciences, and American Association for the Advancement of Science.
Arthur J. Olson
Professor
Arthur Olson is the Anderson Research Chair Professor at the Scripps Research Institute, where 35 years ago he founded and still directs the Molecular Graphics Laboratory. His lab has created both AutoDock and AutoDock Vina, the world's most widely used and cited molecular docking programs. Olson is the Director of the NIH-funded HIV Interaction and Viral Evolution (HIVE) Center. He initiated the volunteer computing HIV project, FightAIDS@Home, in 2000, which has run on IBM's World Community Grid since 2005.
Stefano Forli
Staff Scientist
Dr. Stefano Forli is a Staff Scientist in Prof. Olson's laboratory at TSRI, which he joined in 2008. He received his Ph.D in 2006 in Medicinal Chemistry at the Universita' degli Studi di Siena, Italy. His main expertise is in docking, high throughput virtual screening and structure-activity relationships. The main goal of his research is to exploit structural information for drug discovery to find novel molecules able to bind to and inhibit HIV proteins.
Pierrick Craveur
Research Associate
Dr. Pierrick Craveur joined Prof. Olson's laboratory in 2016 as a Research Associate. He received his Ph.D in 2014 in Computational Structural Biology at Paris Diderot University. He is an expert in protein structure, molecular modeling, and molecular dynamic simulation. His research is focused on protein structures and prediction of their flexibility to find interaction sites between drugs and HIV protein targets.
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Collaborators
There are 14 laboratories in 8 institutions around the U.S. that collaborate on HIV research through the HIVE Center. The HIVE Center comprises a group of investigators with expertise in HIV crystallography, virology, molecular biology, biochemistry, synthetic chemistry and computational biology. We study the mechanistic implications of viral macromolecular interactions and dynamics and its broader impacts of the evolution of drug resistance to address several biological questions:
- How do structures of the HIV polyprotein precursors direct assembly, maturation, and replication?
- What novel HIV-Host interactions drive DNA replication and integration?
- How does dynamics impact viral function and fitness and how can it be exploited for therapeutic targeting?
- What are the structural and dynamic consequences of resistance mutations in the HIV life cycle?
For details of the research of each of these investigators, please visit: hivecenter.org
Ronald M. Levy
Professor
Ronald M. Levy is Laura H. Carnell Professor and Director of the Center for Biophysics and Computational Biology at Temple University, Philadelphia, PA. Before moving to Temple in 2014, he was Board of Governors Professor of Chemistry at Rutgers University. Levy is one of the founding members of the group of scientists who developed molecular dynamics simulations of proteins into the powerful technique used in biophysics and structural biology that it is today. Using computational statistical mechanics as a framework, he has been a leader in studying solvation effects in chemistry and biophysics, and in developing free energy methods and effective potentials for simulating protein-ligand binding. His group developed the Impact commercial software package used for many years by Schrodinger Inc. as an integral part of their docking suite, and the academic Impact package which performs protein-ligand binding free energy simulations using the BEDAM technology.
Nanjie Deng
Assistant Professor
Dr. Nanjie Deng is an Assistant Professor at Pace University. The main focus of his research is to use computer simulation and statistical mechanics to provide atomistic insights on protein-small molecule interaction and protein-protein association to inform structure based drug design and to understand the molecular basis of drug resistance mutations in HIV targets.
Qinfang Sun
Postdoctoral Researcher
Dr. Qinfang Sun is a Research Scientist at Ron Levy's group. Her major research interests are the interactions and the binding mechanisms of proteins/small-molecule ligands using molecular dynamics modeling. The focus of research is to estimate the binding affinity of ligands to protein active sites, which could optimize potential lead compounds with a considerable gain in time and cost.
Bin Zhang
Associate Research Professor
Bin Zhang is an associate research professor from Ron Levy's Group at Temple University. He holds a Ph.D degree in physics from the University of Pittsburgh. Bin joined Dr. Levy's group in 2013. His research focuses on developing advanced sampling and reweighting algorithms in biophysics and computer simulations.
Avik Biswas
Graduate Student
Avik Biswas is currently a Ph.D (Physics) student in the Ron Levy group at Temple University, Philadelphia. Prior to joining the Levy group in 2016, Avik completed his Integrated BS-MS from the Indian Institute of Science Education and Research (Bhopal, India) where his research involved using molecular dynamics and ab initio methods (Density Functional Theory) to understand the mechanics of rolling graphene. Currently, his research is focused on using Potts Hamiltonian models of protein evolutionary fitness to study the inter-relations between protein sequence, structure, and fitness, with a particular interest in the evolution of drug resistance in HIV.
Shima Arasteh
Graduate Student
Shima Arasteh is a Ph.D student from Ron Levy's group at Temple University. She holds a bachelor's degree in physics and a master's degree in biophysics from the University of Tehran. Before joining Dr. Levy's group in 2015, her research focused on the functions and stability of membrane ion channels. Currently, she is studying the conformational transitions of protein kinases, and developing advanced algorithms to measure the free energy changes of these transitions.
Previous Research Team Members
Junchao Xia
Associate Research Professor
Dr. Junchao Xia is a Research Scientist at Ron Levy's group. He is one of the main developers for Academic IMPACT and porting it to World Community Grid. His major research interests are protein-ligand interactions and developments of advanced sampling methods for computer simulations.
William Flynn
Graduate Student
William is a Graduate Student in the Department of Physics and Astronomy at Rutgers University studying under Ron Levy. His research is focused on developing models to understand the fitness of proteins, and the development and application of large-scale parallelized computations.
Di Cui
Assistant Research Professor
Dr. Di Cui is a computational chemist with an interest in biomolecular modeling. Currently, he is an assistant research professor in the Department of Chemistry, Center for Biophysics and Computational Biology, Temple University. His research has been focused on understanding the mechanisms and estimation the binding affinity of small-molecule ligands to protein active sites using molecular dynamic simulations. His current work involves the application of molecular modeling techniques to analyze the binding affinities to the target proteins, with the goal to design new ligand molecules that could serve as leads and optimized compounds for drug discovery.