LDI software and tools

The Lead Discovery Informatics team administers, manages, and implements a suite of chemically aware software tools for collection, analysis, screening, and data handling. LDI offers orientation and user-training for all the resources in their portfolio to members of the St. Jude research community. For questions, training requests, or additional information, please contact the LDI team at SPLDI@stjude.org.

Software Highlights:

• Titian/Mosaic. State-of-the-art, industry standard, sample management platform to track, store, and manage large chemical libraries
• PerkinElmer Electronic Notebook. Asset specifically geared toward chemists and chemical synthesis

Additional LIMS Software:

• ChemBioOffice (Enterprise)

Software Highlights:

• Tibco Spotfire. Data visualization, prediction, and analytical software—chemically aware for analysis of chemical scaffolds
• Biovia Pipeline Pilot. Platform to design robust workflows for manipulating, capturing and analyzing data from multiple sources and dimensions

Additional Software:

• GraphPad (Prism)

Software Highlights:

• MestRenova and MestRenova Console API. A powerful suite of spectral analysis tools uniquely suited for chemists

Software Highlights:

• MOE and Schrodinger. Molecular operating environments for computer-aided design for small molecules, peptides, and biologics with capabilities for ligand-based design, virtual screening, structural bioinformatics, etc.
• DOCK. Platform for predicting ligand binding integrated on the SJ Computing Cluster to facilitate ultra-high-throughput analysis
• Amber. Suite of programs for molecular dynamics simulation with 10x speed improvement over traditional approaches

Additional Software:

• Pymol
• Cresset Systems (Forge, Spark, etc.)

Software Highlights:

• PIMS (Pathology Interface for Mass Spectrometry). Image application for 2D mass profiling and spatial analysis of drug distribution in tissues
• Biotek/Lionheart Fx. Cell-based microscopy platform for high content screening

Software Highlights:

• CDD (Collaborative Drug Discovery). A vault to organize biological and chemical structures data for analysis, visualization, and collaboration – providing support for screening-based grants
• (CCDC) Cambridge Crystallopgraphic Data Centre / (CSD) Cambridge Structural Database. Platform for analyzing biomolecular-small molecule complexes and facilitating structure-based design
• NextMove/Arthor. Next-generation chemical searching tool that provides billions of results in seconds using a chemical pattern-matching engine

Additional Software:

• ChemBI

Software Highlights:

• ADMET Predictor. Physiochemical property prediction tool capable of predicting over 175 chemical properties with AI-driven drug design and development
• Chemprop(++). Chemically aware neural network for molecular property prediction

Additional Software:

• DeepChem

More resources:

pySCA. Drug discovery tool capable of identifying allosteric or cryptic sites of regulation in proteins

SCIEX Systems. Mass spectrometry software that transforms LC-MS/MS worksflows into actionable data