This $786,132 federal Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) will fund the continued development and expansion of several computational tools and applications for the biomedical research community. The key products and services to be delivered include: Further enhancing the functionality of the CHARMM-GUI web-based platform to support more force fields, QM/MM interface for enzymatic...
This $306,872 Project Grant awarded by the National Institute of General Medical Sciences (NIGMS) under CFDA 93.859 Biomedical Research and Research Training Program aims to develop an improved 3D ligand similarity scoring methodology that accounts for water molecules in protein-ligand binding. The grantee, Simulations Plus Inc., will adapt their existing water prediction and ligand displacement algorithms to create a "solvation-informed" shape matching program. This new approach...
This $788,238 Project Grant awarded by the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training Program (CFDA 93.859) supports the development of machine-learning-based and physics-based electronic structure and molecular simulation methods for multiscale modeling of enzymatic reactions and bioimaging probes. The key products to be delivered include: (1) robust active-learning protocols for training machine-learning potentials for ground...
The National Institutes of Health (NIH) National Institute of General Medical Sciences (NIGMS) awarded a 5-year, $138,334 Project Grant (CFDA 93.859 - Biomedical Research and Research Training) to the University of Southern California (USC) to develop a scalable computational platform for ligand discovery. The research aims to combine structure-based and data-driven approaches to enable rapid identification of selective and potent ligands for novel therapeutic targets across areas like pain,...
This Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) will support the development of computational models and machine learning approaches for the rational design of carbohydrate-based drugs and nucleic acid-based imaging agents. The total funding amount is $365,630, with the award period running from September 10, 2024 to July 31, 2029. The project aims to create large, high-quality datasets...
This federal Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) provides $211,988 to develop and test algorithms for iteratively docking subsets of ultra-large small molecule libraries against biological targets. The goal is to significantly reduce the number of molecules that need to be explicitly docked while enriching the docked subset with promising drug candidates. The project aims to overcome...
The National Institute of General Medical Sciences (NIGMS) awarded a $455,870 project grant (CFDA 93.859 Biomedical Research and Research Training) to the Research Foundation of the City University of New York (RFCUNY) doing business as RFCUNY - Brooklyn College. The award, titled "ENHANCING DRUG DISCOVERY RESEARCH BY FREE ENERGY MODELING," aims to expand the use of advanced computational binding free energy models for protein-drug interactions in academic and industrial drug discovery...
This $385,700 five-year Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) will support the development of novel computational approaches for pharmacogenomics research on complex diseases. The key objectives include: 1) Devising advanced deep learning models to predict molecular and phenotypic effects of genetic and chemical perturbations on disease models, 2) Leveraging large language models to...
The National Institute of General Medical Sciences (NIGMS) awarded a $467,947 Project Grant to the University of Colorado-Denver under CFDA 93.859 (Biomedical Research and Research Training program) to create bioinformatics tools that facilitate identifying genetic variants contributing to adverse drug reactions (ADRs). The key products to be delivered include: 1) A protein docking server to assess how drug variants could cause potential side effects, and 2) Online tools to identify specific...
The National Institute of General Medical Sciences (NIGMS) awarded a $314,363 Project Grant under the Biomedical Research and Research Training program (CFDA 93.859) to Delineate Inc. The project, titled "DELINEATEQSP: ACCELERATING QUANTITATIVE SYSTEMS PHARMACOLOGY MODEL BUILDING AND REPURPOSING", aims to develop an innovative platform that uses large language models (LLMs) to streamline the construction and repurposing of quantitative systems pharmacology (QSP) models from...
This $752,456 Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) supports the development and application of innovative computational technologies for the design of small-molecule ligands. The key products and services to be delivered over the 5-year project period include:
Creating a large database of predicted protein-ligand complexes to improve the accuracy of structure-based machine learning models for assessing small-molecule binding and suggesting lead optimization strategies tailored to specific proteins.
Developing new online tools and methods for streamlining the use of computer-aided drug discovery (CADD) approaches, making them more accessible to the broader scientific community, including through increased language translation, accessibility features, and mentoring opportunities.
Continued validation and application of the research team's CADD tools through collaborations with academic and industry partners across diverse protein systems implicated in protein synthesis, metabolism, cancer, viral infections, and other areas of biological and medical importance.
By advancing the accuracy, accessibility, and adoption of CADD technologies, this project aims to accelerate the discovery and development of new small-molecule probes and drug candidates to improve human health.