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Shelat Lab: LDI Center

Who We Are

Lead Discovery Informatics Team
The Lead Discovery Informatics (LDI) Center consists of members with advanced training in computational chemistry, functional data analysis, applied mathematics, and information sciences. We have professional experience in computer-aided molecular design, quantitative structure-activity relationship analysis, scientific application programming, laboratory information management, and the management of scientific collaborations.

What We Do

  1. Computer-aided molecular design, using such methods as molecular docking and chemical similarity searching
  2. Molecular modelling, including the application of molecular dynamics and quantum mechanics
  3. Development and validation of quantitative structure-activity models for compound optimization
  4. Development of new algorithms to model molecular interactions and drug efficacy
  5. Development of new tools for visualizing and analyzing multi-dimensional data sets
  6. Data integration between drug sensitivity and 'omics' data generated by other departments
  7. Pathway perturbation modeling and network analysis
  8. High-content assay image analysis
  9. Building robust workflows and data pipelines for lab automation
  10. Laboratory information management (e.g., chemical inventory and registration, electronic notebooks, etc.)

How We Collaborate

The entry points for collaborating with our group are illustrated below:

LDI Process

Molecules

Given one or more molecules, we can use tools from computational chemistry and chemical informatics to do the following: (a) identify analogs from public repositories or commercial catalogs using chemical similarity search methods; (b) annotate input molecules with predicted physicochemical properties (e.g., chemical reactivity, druglikeness, and assay interference potential), or with reported or inferred biological activity using public and proprietary databases; (c) use pharmacophore approaches to build models of binding to biological targets; (d) develop statistical models relating chemical properties to experimentally observed behavior such as binding affinity or solubility.

Biological Target

Given one or more biological targets, we can do the following: (a) dock virtual libraries against the target(s) to identify potential binders; (b) analyze conformational flexibility or conserved water networks using molecular dynamics; (c) develop homology models; (d) analyze the target for potential binding sites and small-molecule druggability.

Assay Data

Given one or more assay data sets, we can do the following: (a) use functional data analysis to model the data according to a defined mathematical process, (b) help visualize and interpret the data using techniques from exploratory data analysis; (c) use machine learning to train and validate statistical models that predict class labels within the data set; (d) connect scientists to relevant and accessible software tools that are managed by LDI.

We manage chemo-centric software applications for the institution and provide both basic and advanced training for certain applications, such as Pipeline Pilot and Electronic Notebook. View a complete list of software resources. Please contact the LDI center for more information.

Additionally, we have created an online database, eDrugs portal, where you can search the St. Jude chemical library and our database of high-throughput screening experiments.

Laboratory Workflow

We can assist with the following: (a) deploying existing LDI-managed laboratory information management services (LIMS) to your lab or a specific laboratory workflow, such as routinely run assays; (b) developing software applications for data pipelines, ensuring proper data capture, QC, and facilitate analysis at decision points; (c) data warehousing or legacy or new data.

Resource Management

Most routine analysis (estimated analysis time <5 days) does not require a dedicated full-time equivalent (FTE) and can be handled by our LDI staff, usually on a first come-first serve basis. However, if we estimate that a substantial investment of time is required, or if an investigator requests dedicated support, then the investigator must provide grant support for the project. Grant funds are used to support staff salaries and to defray the cost of LDI-managed software resources. Furthermore, our free one-on-one and group training sessions for LDI-managed software resources are an additional way to consult and collaborate with our team. 

Our center maintains a number of software applications that are accessible to the St. Jude research community. See this list (LDI software resources) for more details and instructions. Existing users, may join one of our user groups in order to receive the latest updates and notices of downtime.