BioDockify Pharma AI

AI Research Assistant for Pharmaceutical Sciences

15 integrated research modules. 4 specialized sub-agents. Persistent memory across your entire PhD. AutoDock Vina + MM-GBSA docking, SPSS-level statistics, QSAR modeling, pharmacophore screening, and academic writing — all in one platform.

Docker Ready v6.9.5 15 Modules

⚡ Get Started View on GitHub →

⟩ Quick Start

        # The -v flag is REQUIRED. Without it, ALL data is lost on container delete.

        $ mkdir ~/biodockify-backups

        $ docker run -d -p 80:80 --name biodockify-pharma \\

          -v biodockify_pharma_usr:/a0/usr \\

          -v ~/biodockify-backups:/app/data \\

          tajo9128/biodockify-pharma-ai:latest

        # Visit http://localhost

⟩ Why BioDockify Pharma AI

🧬

Molecular Docking + MM-GBSA

AutoDock Vina integration with automatic MM-GBSA free energy scoring. Multiple input formats (PDB, SMILES, SDF). CPU-only, no GPU required.

📊

SPSS-Level Statistics

20 analysis types + auto-analyze mode. Descriptive, correlation, group tests, normality, PCA, survival, meta-analysis — all built in.

📚

Literature Intelligence

10-database search (PubMed, Semantic Scholar, arXiv, OpenAlex). PRISMA screening, BioNER, 36,145-journal recommender.

✍️

Academic Writer

8-tab writer: Lit Review, Paper, Thesis, Grant Writer, Regulatory, Citation Manager, Lecture, Slides generation.

🧠

QSAR & Pharmacophore

6 regression + 3 classification models, batch predict, read-across. Protein-based pharmacophore screening with target ID.

🐬

Docker Native

One command to run (-p 80:80). Data persists forever with Docker volumes. No installation required.

⟩ 15 Consolidated Research Modules

#	Module	Function	Backend
1	Research Command Center	Auto-research pipeline + Literature Search + Wet Lab tracking	23 REST endpoints
2	Molecular Toolkit	ADMET + SwissADME + BOILED-Egg + Bioavailability Radar + Docking (Vina + MM-GBSA) + Inline 3D Analysis	RDKit + Vina + Meeko
3	Statistics	20 analysis types + auto-analyze + data transform	scipy + scikit-learn + pandas
4	Academic Writer	8-tab: Lit Review, Paper, Thesis, Grant, Regulatory, Citations, Lecture, Slides	Thesis + Slides + Grant APIs
5	Faculty CMD	9 tabs: Syllabus, Lectures, Tasks, Semester, Lesson, Notes, Slides, Plagiarism, Questions (MCQ/SA/LA/TF + Bloom's)	faculty_tools
6	Journal Finder	36,145 Scopus/WoS journals + verify + fake website detector + dossier + suggest	journals.db + 6 live APIs
7	QSAR Modeler	6 regression + 3 classification, batch predict, read-across, Williams Plot, PLS VIP	RDKit + scikit-learn
8	Pharmacophore	5 tabs: Protein-based, Screen, Batch, Models, Target ID	RDKit
9	Drug Analysis	3Dmol.js viewer (7 styles) + hERG/AMES/pKa/BBB + PAINS/Brenk/NIH + Bioisostere Mutagenesis	RDKit + PubChem
10	Docking Analysis	3D receptor+ligand viewer, H-bonds, surface, interaction SVG, PLIF, RMSD clusters	3Dmol.js + RDKit
11	Knowledge Base	NotebookLM-style document cards, ChromaDB vector search, semantic search	ChromaDB
12	Notebook	KB Search, Podcast (edge-tts), Document Storage, Slide Decks, Video Summaries, RAG Chat	ChromaDB + edge-tts + FFmpeg
13	System Health	Platform-aware badges (Vina + MM-GBSA + RDKit + Meeko), Docker vs Windows	health.py
14	Deep Research	5-database collection (PubMed, Semantic Scholar, Crossref, OpenAlex, arXiv)	5 live APIs
15	Backup & Recovery	Full backup/restore with preview + auto-backup on first health check	backup APIs

⟩ 4 Specialized Sub-Agents

🔬

Researcher

Deep research, literature synthesis, drug discovery. 10 literature APIs, PRISMA, BioNER

📈

Biostatistician

SPSS-level analysis, clinical trials, PK/PD modeling. 20 types, PCA, survival, meta-analysis

📝

Writer

Academic writing, thesis, papers, slides. 36,145-journal database

💻

Hacker

Code execution, web scraping, automation, debugging

⟩ Research Workflow

User Request
↓
Agent0 (Main Orchestrator)
↓
├→ Researcher → Hacker (if blocked)
││││││││││↓
│││││Biostatistician (SPSS-level) + QSAR (predictions)
││││││││││↓
│││││Pharmacophore (feature detection)
││││││││││↓
├→ Molecular Toolkit (Docking: Vina → MM-GBSA → Deep Analysis)
││││││││││↓
├→ Pipeline Engine (25-stage: Debate → Experiment → Self-Heal → Verify → HITL)
││││││││││↓
└→ Writer + Journal Recommender (36,145) + Mol Optimizer

⟩ Your Data Persists Forever

🧠

Memory

FAISS vector DB

💬

Chat History

All conversations

⚙️

Settings

Your preferences

🔑

API Keys & Secrets

Secure storage

📚

Knowledge Base

ChromaDB vectors

📁

Projects

All your work

📄

Workdir Files

Saved outputs

🧩

User Plugins & Skills

Custom extensions