BioProtIS

BioProtIS streamlines protein-ligand interaction analysis by integrating molecular dynamics and docking to automate workflows at genomic and transcriptomic scales.

Key Features:

• Inverted Virtual Screening (IVS): The pipeline employs an IVS approach for computational screening of bioproducts, biological systems, and therapeutic drugs.
• Molecular Dynamics Integration: Integrates molecular dynamics analyses to ensure protein structures are energetically favorable and representative of stable conformations.
• Docking Integration: Incorporates docking analyses to evaluate ligand-protein interactions.
• Multiple Testing Scenarios: Accommodates blind docking or site-specific targeting for applications including drug repositioning, exploration of new allosteric binding sites, and toxicity assessments.
• Multi-substrate Evaluation: Enables simultaneous evaluation of multiple substrates to optimize the discovery process.
• Modular Architecture: Supports custom modifications and lays the foundation for integration of diverse docking algorithms.

Scientific Applications:

• Genomic-scale Analysis: Facilitates streamlined docking of ligands with proteins sourced from genomes, as demonstrated with the genome of Homo sapiens.
• Transcriptomic-scale Analysis: Automates protein-ligand interaction analysis at transcriptomic scales, as demonstrated with transcriptomes of Cereus jamacaru and Aspisoma lineatum.
• Bioproduct Discovery: Supports high-throughput computational screening for discovery of potential bioproducts.
• Drug Repositioning: Site-specific targeting capabilities enable identification of new therapeutic applications for existing drugs.
• Allosteric Binding Site Exploration: Blind docking capabilities support discovery of new allosteric binding sites.
• Toxicity Assessment: Testing scenarios support evaluation of compound toxicity profiles.

Methodology:

The pipeline integrates Modeller, AlphaFold, Gromacs, FPOCKET, and AutoDock Vina. Molecular dynamics and docking analyses are combined to ensure protein structures are energetically favorable and representative of stable conformations. The pipeline automates input and output integration for virtual screening.