Using advanced computational hardware and software, this core provides resources for structure prediction, molecular modeling, simulation, virtual screening, and data analysis.

Cost structure: Initial exploratory modeling and pilot virtual screening can be performed at no cost. For follow-up studies (expanded screening, production simulations, optimization, etc.), we expect for relevant computational personnel effort to be included in grant applications or other supported funding.

Structure Prediction & Complex Modeling

Predict protein structures and assemblies, assess confidence, and generate starting models for downstream studies.
Examples: AlphaFold2(-Multimer), AlphaFold3, ROSETTA/RoseTTAFold, MODELLER.

Virtual Screening & Molecular Docking

Structure-based docking and screening workflows, including scoring/rescoring, filtering, enrichment analysis, and custom pipelines for prioritized purchasing.
Examples: DOCK 3.x/6, RDKit workflows.

Molecular Dynamics Simulations

Atomistic and coarse-grained simulations, enhanced sampling, trajectory analysis, binding pathway studies, and free-energy computations.
Examples: OpenMM, GROMACS, AMBER, NAMD; analysis with MDAnalysis, MDTraj, VMD.

Cheminformatics & ML

Similarity search, clustering, library design, QSAR/ADMET, and data pipelines for hit triage and SAR.
Examples: RDKit, scikit-learn, DeepChem, Chemprop; ADMET tools as available.

High-Performance Computing

Access to USF Research Computing clusters and GPU resources, job orchestration, storage strategy, and reproducible runs.