A world-class collaborative research center with expertise in chemical informatics, molecular simulation, computer-aided molecular design, and chemically aware machine learning.
The mission of the Lead Discovery Informatics (LDI) center is to enable a deeper interrogation of biology through the integration of chemistry, computation, and data science.
LDI builds and maintains the chemo-centric informatics infrastructure for St. Jude by doing the following: (a) developing and applying algorithms to model molecular interactions and predict drug efficacy; (b) designing and implementing tools for visualizing and analyzing molecular properties and relationships; (c) constructing robust workflows and data pipelines for lab automation and complex data analysis; and (d) deploying, customizing, and maintaining laboratory information management systems (LIMS).
The scientific staff in LDI came from diverse career backgrounds and have extensive expertise in computational chemistry, chemical informatics, applied mathematics, and computer science. We collaborate with scientists from different fields by using chemically aware computation to design, execute, and analyze experiments. Examples of recent projects include: (a) performing an all-atom molecular dynamics simulation of a membrane protein immersed in water and a lipid bilayer to understand the consequence of mutations on protein function and binding to ligands; (b) using density functional theory to model molecular orbital occupancy and to predict chemical reactivity; (c) developing a flexible yet parsimonious closed-form equation to model two and three-dimensional drug response surfaces; (d) building a database containing approximately 7 million screening results from the St. Jude chemical library; (e) deploying a non-relational database that leverages within-memory computation to enable searching within seconds of over 1,000,000,000 available small molecules by substructure or chemical similarity; (f) using neural networks trained on molecular topology to discriminate between biologically active and inactive small molecules; and (g) developing a next generation compound library for drug discovery using chemical informatics approaches
We are pioneering new solutions to tackle novel and difficult targets for small molecule drug discovery. We are developing and applying our expertise in the areas of machine learning, ultra large scale docking, and the design of next generation small molecule-DNA modulators. These efforts push current boundaries and speed projects to successful outcomes.
Jason Ochoada, Cheminformatics Scientist
Dr. Shelat graduated from Harvard in 2000 with a Bachelor of Arts degree in the Biochemical Sciences. He received his PhD from the Chemistry and Chemical Biology department at the University of California, San Francisco in 2005 where he studied chemical informatics and computer-aided drug design as a joint student with Kip Guy and Tack Kuntz. He joined St. Jude as a postdoctoral fellow in 2005, became an Assistant Member of the faculty in 2010, and was promoted to Associate Member in 2016. In addition to leading the LDI group, Dr. Shelat also manages his own wet lab and runs a joint laboratory with Dr. Christopher Tinkle from the Department of Radiation Oncology. His research program uses the tools of chemical informatics, computational biology, and chemical biology to investigate the mechanism of drug action and to target disease vulnerabilities, with the ultimate goal of translating laboratory findings into human clinical trials.
CBT has shown me that there is a huge opportunity for growth in the way scientific data is analyzed and shared. Many scientific departments don’t have a dedicated team of informatics scientists working hand in hand with researchers on the tools used to analyze their data, and so most researchers necessarily rely on simple or out-of-the-box tools. In CBT, however, we have the opportunity to customize the tools we use to analyze experimental data, and fully realize the potential of those experiments. It’s really exciting.
Nathaniel Twarog, Cheminformatics Analyst