Our Core In Silico Services
Accelerating therapeutic discovery through artificial intelligence, biophysical structural modeling, and advanced multi-omics bioinformatics.
AI-Driven Drug Discovery
Integrating artificial intelligence with computational biology to accelerate therapeutic discovery, repurpose existing drugs, and prioritize novel chemical scaffolds.
Traditional drug screening entails extensive timelines and high attrition rates. ProGen applies machine learning architectures and deep neural networks to vast chemical spaces, predicting bioactivity, identifying potential off-target effects, and accelerating lead generation.
Technical Capabilities:
- ✔ Drug Repurposing & Lead Identification: Machine learning screening of approved drugs and clinical candidates for novel therapeutic indications.
- ✔ AI/ML-Based Predictive Modeling: Quantitative Structure-Activity Relationship (QSAR) and graph neural networks for affinity prediction.
- ✔ Chemical Library Prioritization: Screening millions of small-molecule compounds down to high-confidence candidate cohorts.
Structure-Based Drug Design (SBDD)
From target structure resolution to lead optimization through advanced molecular modeling, docking, and all-atom molecular dynamics simulations.
We examine the thermodynamic and conformational realities of macromolecular complexes. By coupling rigid/flexible molecular docking with multi-nanosecond MD trajectories and MM/GBSA free energy calculations, we quantify binding affinity with high biophysical accuracy.
Technical Capabilities:
- ✔ Protein Modeling & Engineering: Homology modeling, structural refinement, loop modeling, and binding pocket characterization.
- ✔ Molecular Docking & HTVS: Target-ligand and protein-protein docking across diverse conformer ensembles.
- ✔ Advanced Molecular Dynamics (MD): 100ns to 1μs explicit-solvent simulations to evaluate conformational stability and RMSD/RMSF.
- ✔ Binding Free Energy Calculations: Molecular Mechanics Generalized Born Surface Area (MM/GBSA) and per-residue decomposition.
Multi-Omics Data Analysis
Transforming complex high-throughput omics data into meaningful biological insights through advanced bioinformatics and systems biology.
Next-generation sequencing and high-density mass spectrometry yield complex, multidimensional datasets. We deconvolute this biological complexity to reveal differentially regulated genes, enriched signaling cascades, and robust candidate biomarkers.
Technical Capabilities:
- ✔ Genomics, Transcriptomics & Proteomics: End-to-end processing of raw sequencing reads (FASTQ) and quantitative proteomic profiles.
- ✔ NGS Data Processing: Quality control, alignment to reference genomes (GRCh38), count normalization, and differential expression analysis (DESeq2/edgeR).
- ✔ Functional Annotation & Pathway Enrichment: Gene Ontology (GO), KEGG, Reactome, and Gene Set Enrichment Analysis (GSEA).
- ✔ Biomarker Discovery & Network Biology: Protein-protein interaction (PPI) network construction and hub gene identification.
Custom Computational Solutions
Building scalable, reproducible, and intelligent computational infrastructure for modern life science and biomedical research.
Non-standard research designs require bespoke software workflows. We develop custom computational pipelines, automated data parsing tools, and tailored analytics environments that integrate seamlessly with your research infrastructure.
Technical Capabilities:
- ✔ Custom Bioinformatics Pipelines: Automated data transformation, quality filtering, and standardized execution pipelines.
- ✔ Workflow Automation & Reproducibility: Scalable batch processing minimizing manual intervention and human error.
- ✔ Linux-Based Computing Solutions: High-performance cluster setup, multi-threaded parallel execution, and cloud compute optimization.
- ✔ Scientific Programming & Scripting: Custom implementations in Python, R, MATLAB, and Bash.