diff --git a/.gitignore b/.gitignore
index 08972f38..04ce48ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -142,6 +142,7 @@ vite.config.ts.timestamp-*
 *~
 .venv/
 venv/
+__pycache__/
 
 # Visual Studio Code
 .vscode/
diff --git a/backend/__init__.py b/backend/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/backend/auth.py b/backend/auth.py
new file mode 100644
index 00000000..de16eeaa
--- /dev/null
+++ b/backend/auth.py
@@ -0,0 +1,19 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from fastapi import Header, HTTPException, status
+from typing import Optional
+
+
+async def get_forwarded_user(x_forwarded_user: Optional[str] = Header(None, alias="X-Forwarded-User")) -> str:
+    """Extract authenticated user from X-Forwarded-User header"""
+    if not x_forwarded_user:
+        raise HTTPException(
+            status_code=status.HTTP_401_UNAUTHORIZED,
+            detail="Missing X-Forwarded-User header. Authentication required.",
+        )
+    return x_forwarded_user
diff --git a/backend/database/__init__.py b/backend/database/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/backend/database/engine.py b/backend/database/engine.py
new file mode 100644
index 00000000..194a65ae
--- /dev/null
+++ b/backend/database/engine.py
@@ -0,0 +1,51 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+##########################################################################
+
+from sqlalchemy.ext.asyncio import create_async_engine, AsyncSession, async_sessionmaker
+from sqlalchemy.exc import OperationalError
+from sqlalchemy.orm import declarative_base
+import os
+
+if "MARIADB_HOST" not in os.environ:
+    engine = AsyncSessionLocal = None
+else:
+    DB_USER = os.getenv("MARIADB_USER", "user")
+    DB_PASSWORD = os.getenv("MARIADB_PASSWORD", "password")
+    DB_HOST = os.getenv("MARIADB_HOST", "localhost")
+    DB_PORT = os.getenv("MARIADB_PORT", "8080")
+    DATABASE_URL = f"mysql+aiomysql://{DB_USER}:{DB_PASSWORD}@{DB_HOST}:{DB_PORT}"
+
+    try:
+        engine = create_async_engine(
+            DATABASE_URL,
+            echo=True,
+            pool_size=10,
+            max_overflow=20,
+            pool_pre_ping=True,
+            pool_recycle=3600,
+        )
+
+        AsyncSessionLocal = async_sessionmaker(engine, class_=AsyncSession, expire_on_commit=False)
+    except OperationalError:
+        engine = AsyncSessionLocal = None
+
+Base = declarative_base()
+
+
+async def get_db():
+    if AsyncSessionLocal is None:
+        yield None
+        return
+    async with AsyncSessionLocal() as session:
+        try:
+            yield session
+            await session.commit()
+        except Exception:
+            await session.rollback()
+            raise
+        finally:
+            await session.close()
diff --git a/backend/database/models.py b/backend/database/models.py
new file mode 100644
index 00000000..b0bc610b
--- /dev/null
+++ b/backend/database/models.py
@@ -0,0 +1,71 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from sqlalchemy import Column, String, DateTime, Boolean, ForeignKey, Index, Text, JSON, Float
+from sqlalchemy.orm import relationship, Mapped, mapped_column
+from datetime import datetime
+from typing import Optional
+from backend.database.engine import Base
+
+
+class Project(Base):
+    __tablename__ = "projects"
+
+    id: Mapped[str] = mapped_column(String(255), primary_key=True)
+    user: Mapped[str] = mapped_column(String(255), nullable=False, index=True)
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    created_at: Mapped[datetime] = mapped_column(DateTime, default=datetime.utcnow, nullable=False)
+    last_modified: Mapped[datetime] = mapped_column(
+        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False
+    )
+
+    experiments: Mapped[list["Experiment"]] = relationship(
+        "Experiment", back_populates="project", cascade="all, delete-orphan"
+    )
+
+    __table_args__ = (Index("idx_user_last_modified", "user", "last_modified"),)
+
+
+class Experiment(Base):
+    __tablename__ = "experiments"
+
+    id: Mapped[str] = mapped_column(String(255), primary_key=True)
+    project_id: Mapped[str] = mapped_column(String(255), ForeignKey("projects.id", ondelete="CASCADE"), nullable=False)
+    user: Mapped[str] = mapped_column(String(255), nullable=False, index=True)
+    name: Mapped[str] = mapped_column(String(255), nullable=False)
+    created_at: Mapped[datetime] = mapped_column(DateTime, default=datetime.utcnow, nullable=False)
+    last_modified: Mapped[datetime] = mapped_column(
+        DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False
+    )
+    is_running: Mapped[Optional[bool]] = mapped_column(Boolean, default=False)
+
+    # System state fields
+    smiles: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    problem_type: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    problem_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    system_prompt: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    problem_prompt: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    property_type: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    custom_property_name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
+    custom_property_desc: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    custom_property_ascending: Mapped[Optional[bool]] = mapped_column(Boolean, nullable=True)
+
+    # Complex JSON fields for nested data structures
+    tree_nodes: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    edges: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    metrics_history: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    visible_metrics: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    graph_state: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+    auto_zoom: Mapped[Optional[bool]] = mapped_column(Boolean, nullable=True)
+    sidebar_state: Mapped[Optional[str]] = mapped_column(JSON, nullable=True)
+
+    # Experiment context
+    experiment_context: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+
+    project: Mapped["Project"] = relationship("Project", back_populates="experiments")
+
+    __table_args__ = (Index("idx_user_project", "user", "project_id"),)
diff --git a/backend/database/schemas.py b/backend/database/schemas.py
new file mode 100644
index 00000000..71a63432
--- /dev/null
+++ b/backend/database/schemas.py
@@ -0,0 +1,109 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from pydantic import BaseModel, Field
+from datetime import datetime
+from typing import List, Optional, Any
+
+
+class ExperimentBase(BaseModel):
+    name: str
+
+
+class ExperimentCreate(ExperimentBase):
+    pass
+
+
+class ExperimentUpdate(BaseModel):
+    name: Optional[str] = None
+    is_running: Optional[bool] = None
+
+    # System state fields
+    smiles: Optional[str] = None
+    problem_type: Optional[str] = Field(None, alias="problemType")
+    problem_name: Optional[str] = Field(None, alias="problemName")
+    system_prompt: Optional[str] = Field(None, alias="systemPrompt")
+    problem_prompt: Optional[str] = Field(None, alias="problemPrompt")
+    property_type: Optional[str] = Field(None, alias="propertyType")
+    custom_property_name: Optional[str] = Field(None, alias="customPropertyName")
+    custom_property_desc: Optional[str] = Field(None, alias="customPropertyDesc")
+    custom_property_ascending: Optional[bool] = Field(None, alias="customPropertyAscending")
+
+    # Complex nested data (stored as JSON)
+    tree_nodes: Optional[Any] = Field(None, alias="treeNodes")
+    edges: Optional[Any] = None
+    metrics_history: Optional[Any] = Field(None, alias="metricsHistory")
+    visible_metrics: Optional[Any] = Field(None, alias="visibleMetrics")
+    graph_state: Optional[Any] = Field(None, alias="graphState")
+    auto_zoom: Optional[bool] = Field(None, alias="autoZoom")
+    sidebar_state: Optional[Any] = Field(None, alias="sidebarState")
+
+    # Experiment context
+    experiment_context: Optional[str] = Field(None, alias="experimentContext")
+
+    class Config:
+        populate_by_name = True
+
+
+class Experiment(ExperimentBase):
+    id: str
+    project_id: str = Field(..., alias="projectId")
+    user: str
+    created_at: datetime = Field(..., alias="createdAt")
+    last_modified: datetime = Field(..., alias="lastModified")
+    is_running: Optional[bool] = Field(None, alias="isRunning")
+
+    # System state fields
+    smiles: Optional[str] = None
+    problem_type: Optional[str] = Field(None, alias="problemType")
+    problem_name: Optional[str] = Field(None, alias="problemName")
+    system_prompt: Optional[str] = Field(None, alias="systemPrompt")
+    problem_prompt: Optional[str] = Field(None, alias="problemPrompt")
+    property_type: Optional[str] = Field(None, alias="propertyType")
+    custom_property_name: Optional[str] = Field(None, alias="customPropertyName")
+    custom_property_desc: Optional[str] = Field(None, alias="customPropertyDesc")
+    custom_property_ascending: Optional[bool] = Field(None, alias="customPropertyAscending")
+
+    # Complex nested data
+    tree_nodes: Optional[Any] = Field(None, alias="treeNodes")
+    edges: Optional[Any] = None
+    metrics_history: Optional[Any] = Field(None, alias="metricsHistory")
+    visible_metrics: Optional[Any] = Field(None, alias="visibleMetrics")
+    graph_state: Optional[Any] = Field(None, alias="graphState")
+    auto_zoom: Optional[bool] = Field(None, alias="autoZoom")
+    sidebar_state: Optional[Any] = Field(None, alias="sidebarState")
+
+    # Experiment context
+    experiment_context: Optional[str] = Field(None, alias="experimentContext")
+
+    class Config:
+        from_attributes = True
+        populate_by_name = True
+
+
+class ProjectBase(BaseModel):
+    name: str
+
+
+class ProjectCreate(ProjectBase):
+    pass
+
+
+class ProjectUpdate(ProjectBase):
+    pass
+
+
+class Project(ProjectBase):
+    id: str
+    user: str
+    created_at: datetime = Field(..., alias="createdAt")
+    last_modified: datetime = Field(..., alias="lastModified")
+    experiments: List[Experiment] = []
+
+    class Config:
+        from_attributes = True
+        populate_by_name = True
diff --git a/backend/routers/__init__.py b/backend/routers/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/backend/routers/projects.py b/backend/routers/projects.py
new file mode 100644
index 00000000..02cbf06a
--- /dev/null
+++ b/backend/routers/projects.py
@@ -0,0 +1,243 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+"""
+Serves routes for database interaction for projects and experiments (``/api/projects/*``).
+"""
+from fastapi import APIRouter, Depends, HTTPException
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy import select
+from sqlalchemy.orm import selectinload
+from typing import List
+import time
+import random
+from datetime import datetime
+
+from backend.database.engine import get_db
+from backend.auth import get_forwarded_user
+from backend.database import models, schemas
+
+router = APIRouter(prefix="/api/projects", tags=["projects"])
+
+
+def generate_id(prefix: str) -> str:
+    """Generate unique ID"""
+    timestamp = int(time.time() * 1000)
+    random_str = "".join(random.choices("abcdefghijklmnopqrstuvwxyz0123456789", k=9))
+    return f"{prefix}_{timestamp}_{random_str}"
+
+
+@router.get("/", response_model=List[schemas.Project])
+async def get_projects(user: str = Depends(get_forwarded_user), db: AsyncSession = Depends(get_db)):
+    """Load all projects for the authenticated user"""
+    result = await db.execute(
+        select(models.Project)
+        .where(models.Project.user == user)
+        .options(selectinload(models.Project.experiments))
+        .order_by(models.Project.last_modified.desc())
+    )
+    projects = result.scalars().all()
+    return projects
+
+
+@router.post("/", response_model=schemas.Project)
+async def create_project(
+    project_data: schemas.ProjectCreate, user: str = Depends(get_forwarded_user), db: AsyncSession = Depends(get_db)
+):
+    """Create a new project for the authenticated user"""
+    new_project = models.Project(
+        id=generate_id("project"),
+        user=user,
+        name=project_data.name,
+        created_at=datetime.utcnow(),
+        last_modified=datetime.utcnow(),
+    )
+    db.add(new_project)
+    await db.commit()
+    await db.refresh(new_project)
+    return new_project
+
+
+@router.put("/{project_id}", response_model=schemas.Project)
+async def update_project(
+    project_id: str,
+    project_data: schemas.ProjectUpdate,
+    user: str = Depends(get_forwarded_user),
+    db: AsyncSession = Depends(get_db),
+):
+    """Update a project (only if owned by user)"""
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    project.name = project_data.name
+    project.last_modified = datetime.utcnow()
+
+    await db.commit()
+    await db.refresh(project)
+    return project
+
+
+@router.delete("/{project_id}")
+async def delete_project(project_id: str, user: str = Depends(get_forwarded_user), db: AsyncSession = Depends(get_db)):
+    """Delete a project (only if owned by user)"""
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    await db.delete(project)
+    await db.commit()
+    return {"success": True}
+
+
+@router.post("/{project_id}/experiments", response_model=schemas.Experiment)
+async def create_experiment(
+    project_id: str,
+    experiment_data: schemas.ExperimentCreate,
+    user: str = Depends(get_forwarded_user),
+    db: AsyncSession = Depends(get_db),
+):
+    """Create a new experiment (only if user owns project)"""
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    new_experiment = models.Experiment(
+        id=generate_id("exp"),
+        project_id=project_id,
+        user=user,
+        name=experiment_data.name,
+        created_at=datetime.utcnow(),
+        last_modified=datetime.utcnow(),
+    )
+
+    project.last_modified = datetime.utcnow()
+
+    db.add(new_experiment)
+    await db.commit()
+    await db.refresh(new_experiment)
+    return new_experiment
+
+
+@router.put("/{project_id}/experiments/{experiment_id}", response_model=schemas.Experiment)
+async def update_experiment(
+    project_id: str,
+    experiment_id: str,
+    experiment_data: schemas.ExperimentUpdate,
+    user: str = Depends(get_forwarded_user),
+    db: AsyncSession = Depends(get_db),
+):
+    """Update an experiment (only if user owns it)"""
+    result = await db.execute(
+        select(models.Experiment).where(
+            models.Experiment.id == experiment_id,
+            models.Experiment.project_id == project_id,
+            models.Experiment.user == user,
+        )
+    )
+    experiment = result.scalar_one_or_none()
+
+    if not experiment:
+        raise HTTPException(status_code=404, detail="Experiment not found")
+
+    # Update all provided fields
+    update_data = experiment_data.model_dump(exclude_unset=True, by_alias=False)
+    for field, value in update_data.items():
+        if hasattr(experiment, field):
+            setattr(experiment, field, value)
+
+    experiment.last_modified = datetime.utcnow()
+
+    # Update project's last_modified
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+    if project:
+        project.last_modified = datetime.utcnow()
+
+    await db.commit()
+    await db.refresh(experiment)
+    return experiment
+
+
+@router.delete("/{project_id}/experiments/{experiment_id}")
+async def delete_experiment(
+    project_id: str, experiment_id: str, user: str = Depends(get_forwarded_user), db: AsyncSession = Depends(get_db)
+):
+    """Delete an experiment (only if user owns it)"""
+    result = await db.execute(
+        select(models.Experiment).where(
+            models.Experiment.id == experiment_id,
+            models.Experiment.project_id == project_id,
+            models.Experiment.user == user,
+        )
+    )
+    experiment = result.scalar_one_or_none()
+
+    if not experiment:
+        raise HTTPException(status_code=404, detail="Experiment not found")
+
+    await db.delete(experiment)
+
+    # Update project's last_modified
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+    if project:
+        project.last_modified = datetime.utcnow()
+
+    await db.commit()
+    return {"success": True}
+
+
+@router.patch("/{project_id}/experiments/{experiment_id}/running")
+async def set_experiment_running(
+    project_id: str,
+    experiment_id: str,
+    is_running: bool,
+    user: str = Depends(get_forwarded_user),
+    db: AsyncSession = Depends(get_db),
+):
+    """Set experiment running status (only if user owns it)"""
+    result = await db.execute(
+        select(models.Experiment).where(
+            models.Experiment.id == experiment_id,
+            models.Experiment.project_id == project_id,
+            models.Experiment.user == user,
+        )
+    )
+    experiment = result.scalar_one_or_none()
+
+    if not experiment:
+        raise HTTPException(status_code=404, detail="Experiment not found")
+
+    experiment.is_running = is_running
+    experiment.last_modified = datetime.utcnow()
+
+    # Update project's last_modified
+    result = await db.execute(
+        select(models.Project).where(models.Project.id == project_id, models.Project.user == user)
+    )
+    project = result.scalar_one_or_none()
+    if project:
+        project.last_modified = datetime.utcnow()
+
+    await db.commit()
+    return {"success": True, "is_running": is_running}
diff --git a/backend/routers/webui.py b/backend/routers/webui.py
new file mode 100644
index 00000000..cc7b6717
--- /dev/null
+++ b/backend/routers/webui.py
@@ -0,0 +1,45 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+"""
+Web UI (``/``) routing
+"""
+from fastapi import Request, APIRouter
+from fastapi.responses import HTMLResponse
+from fastapi.staticfiles import StaticFiles
+import os
+from loguru import logger
+
+router = APIRouter(tags=["webui"])
+
+if "FLASK_APPDIR" in os.environ:
+    DIST_PATH = os.environ["FLASK_APPDIR"]
+else:
+    DIST_PATH = os.path.join(os.path.dirname(__file__), "flask-app", "dist")
+ASSETS_PATH = os.path.join(DIST_PATH, "assets")
+
+if os.path.exists(ASSETS_PATH):
+    # Serve the frontend
+    router.mount("/assets", StaticFiles(directory=ASSETS_PATH), name="assets")
+    router.mount("/rdkit", StaticFiles(directory=os.path.join(DIST_PATH, "rdkit")), name="rdkit")
+
+    @router.get("/")
+    async def root(request: Request):
+        logger.info(f"Request for Web UI received. Headers: {str(request.headers)}")
+        with open(os.path.join(DIST_PATH, "index.html"), "r") as fp:
+            html = fp.read()
+
+        html = html.replace(
+            "<!-- APP CONFIG -->",
+            f"""
+           <script>
+           window.APP_CONFIG = {{
+               WS_SERVER: '{os.getenv("WS_SERVER", "ws://localhost:8001/ws")}',
+               VERSION: '{os.getenv("SERVER_VERSION", "")}'
+           }};
+           </script>""",
+        )
+        return HTMLResponse(html)
diff --git a/backend/server.py b/backend/server.py
new file mode 100644
index 00000000..fd612b8a
--- /dev/null
+++ b/backend/server.py
@@ -0,0 +1,50 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+"""
+General server and ``/`` routing infrastructure.
+"""
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from contextlib import asynccontextmanager
+
+from backend.database.engine import engine, Base
+from backend.routers import webui
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    if engine is not None:
+        # Startup: Create tables
+        async with engine.begin() as conn:
+            await conn.run_sync(Base.metadata.create_all)
+
+    yield
+
+    if engine is not None:
+        # Shutdown: Close connections
+        await engine.dispose()
+
+
+app = FastAPI(title="Flask Copilot Backend", lifespan=lifespan)
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=["*"],
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+@app.get("/health")
+async def health_check():
+    return {"status": "healthy"}
+
+app.include_router(webui.router)
+
+if __name__ == "__main__":
+    import uvicorn
+
+    uvicorn.run(app, host="0.0.0.0", port=8001)
diff --git a/charge_backend/backend_helper_funcs.py b/charge_backend/backend_helper_funcs.py
index ef81488b..d5dc072b 100644
--- a/charge_backend/backend_helper_funcs.py
+++ b/charge_backend/backend_helper_funcs.py
@@ -1,9 +1,14 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
 from loguru import logger
 from fastapi import WebSocket
 import asyncio
 import json
 from typing import Dict, Optional, Literal, Tuple
-from dataclasses import dataclass, asdict
 from collections import defaultdict
 
 from charge.clients.autogen import AutoGenAgent
@@ -11,56 +16,7 @@
 from charge.servers import SMILES_utils
 from charge.servers.molecular_property_utils import get_density
 from callback_logger import CallbackLogger
-
-
-@dataclass
-class Node:
-    id: str
-    smiles: str
-    label: str
-    hoverInfo: str
-    level: int
-    parentId: Optional[str] = None
-    x: Optional[int] = None
-    y: Optional[int] = None
-    # Properties
-    cost: Optional[float] = None
-    bandgap: Optional[float] = None
-    yield_: Optional[float] = None
-    highlight: Optional[str] = "normal"
-    density: Optional[float] = None
-    sascore: Optional[float] = None
-
-    def json(self):
-        ret = asdict(self)
-        ret["yield"] = ret["yield_"]
-        del ret["yield_"]
-        return ret
-
-
-@dataclass
-class Edge:
-    id: str
-    fromNode: str
-    toNode: str
-    status: Literal["computing", "complete"]
-    label: Optional[str] = None
-
-    def json(self):
-        return asdict(self)
-
-
-@dataclass
-class ModelMessage:
-    message: str
-    smiles: Optional[str]
-
-    def json(self):
-        ret = asdict(self)
-        if self.smiles is None:
-            if "smiles" in ret:
-                del ret["smiles"]
-        return ret
+from structures import Node, Edge, ModelMessage
 
 
 def get_price(smiles: str) -> float:
diff --git a/charge_backend/charge_server.py b/charge_backend/charge_server.py
index e3d7b198..b9952881 100644
--- a/charge_backend/charge_server.py
+++ b/charge_backend/charge_server.py
@@ -5,24 +5,15 @@
 ## SPDX-License-Identifier: Apache-2.0
 ################################################################################
 
-import asyncio
-from concurrent.futures import ProcessPoolExecutor
 from functools import partial
-from fastapi import FastAPI, WebSocket, WebSocketDisconnect, Request
-from fastapi.responses import HTMLResponse
-from fastapi.staticfiles import StaticFiles
-from fastapi.middleware.cors import CORSMiddleware
+from fastapi import WebSocket, WebSocketDisconnect
 import os
 import argparse
 import httpx
-from charge.servers.server_utils import try_get_public_hostname
 import os
-
-
-import logging
-from aizynthfinder.utils.logging import setup_logger
-
 from loguru import logger
+
+from charge.servers.server_utils import try_get_public_hostname
 from charge.clients.Client import Client
 from charge.experiments.AutoGenExperiment import AutoGenExperiment
 from charge.clients.autogen import AutoGenPool
@@ -36,6 +27,10 @@
 )
 
 from backend_manager import TaskManager, ActionManager
+from backend.server import app
+from backend.routers import projects as projrouter
+
+app.include_router(projrouter.router)
 
 parser = argparse.ArgumentParser()
 
@@ -69,29 +64,10 @@
 )
 
 # Add standard CLI arguments
-Client.add_std_parser_arguments(
-    parser, defaults=dict(backend="openai", model="gpt-5-nano")
-)
+Client.add_std_parser_arguments(parser, defaults=dict(backend="openai", model="gpt-5-nano"))
 
 args, _ = parser.parse_known_args()
 
-app = FastAPI()
-
-# CORS for development
-app.add_middleware(
-    CORSMiddleware,
-    allow_origins=["*"],
-    allow_credentials=True,
-    allow_methods=["*"],
-    allow_headers=["*"],
-)
-
-if "FLASK_APPDIR" in os.environ:
-    DIST_PATH = os.environ["FLASK_APPDIR"]
-else:
-    DIST_PATH = os.path.join(os.path.dirname(__file__), "flask-app", "dist")
-ASSETS_PATH = os.path.join(DIST_PATH, "assets")
-
 reload_server_list(args.tool_server_cache)
 
 app.post("/register")(partial(register_post, args.tool_server_cache))
@@ -108,55 +84,6 @@
         logger.info(f"{status}")
         count += 1
 
-if os.path.exists(ASSETS_PATH):
-    # Serve the frontend
-    app.mount("/assets", StaticFiles(directory=ASSETS_PATH), name="assets")
-    app.mount(
-        "/rdkit", StaticFiles(directory=os.path.join(DIST_PATH, "rdkit")), name="rdkit"
-    )
-
-    @app.get("/")
-    async def root(request: Request):
-        logger.info(f"Request for Web UI received. Headers: {str(request.headers)}")
-        with open(os.path.join(DIST_PATH, "index.html"), "r") as fp:
-            html = fp.read()
-
-        html = html.replace(
-            "<!-- APP CONFIG -->",
-            f"""
-           <script>
-           window.APP_CONFIG = {{
-               WS_SERVER: '{os.getenv("WS_SERVER", "ws://localhost:8001/ws")}',
-               VERSION: '{os.getenv("SERVER_VERSION", "")}'
-           }};
-           </script>""",
-        )
-        return HTMLResponse(html)
-
-
-async def _cancel_task_if_running(
-    action, task: asyncio.Task | None, executor: ProcessPoolExecutor | None
-):
-    if action not in [
-        "compute",
-        "optimize-from",
-        "compute-reaction-from",
-        "recompute-reaction",
-        "recompute-parent-reaction",
-    ]:
-        return
-
-    if task and not task.done():
-        logger.info("Cancelling existing compute task...")
-        task.cancel()
-        try:
-            await task
-        except asyncio.CancelledError:
-            logger.info("Previous compute task cancelled.")
-
-    if executor:
-        executor.shutdown(wait=False, cancel_futures=True)
-
 
 @app.websocket("/ws")
 async def websocket_endpoint(websocket: WebSocket):
@@ -180,9 +107,7 @@ async def websocket_endpoint(websocket: WebSocket):
 
     # set up an AutoGenAgent pool for tasks on this endpoint
 
-    autogen_pool = AutoGenPool(
-        model=model, backend=backend, api_key=API_KEY, base_url=BASE_URL
-    )
+    autogen_pool = AutoGenPool(model=model, backend=backend, api_key=API_KEY, base_url=BASE_URL)
 
     # Set up an experiment class for current endpoint
     experiment = AutoGenExperiment(task=None, agent_pool=autogen_pool)
@@ -223,9 +148,7 @@ async def websocket_endpoint(websocket: WebSocket):
                     handler_func = action_handlers[action]
                     await handler_func(data)
                 else:
-                    logger.warning(
-                        f"Unknown action received: {action} with data {data}"
-                    )
+                    logger.warning(f"Unknown action received: {action} with data {data}")
             except ValueError as e:
                 logger.error(f"Error in internal loop connection: {e}")
                 await task_manager.cancel_current_task()
diff --git a/charge_backend/structures.py b/charge_backend/structures.py
new file mode 100644
index 00000000..66041817
--- /dev/null
+++ b/charge_backend/structures.py
@@ -0,0 +1,59 @@
+################################################################################
+## Copyright 2025 Lawrence Livermore National Security, LLC. and Binghamton University.
+## See the top-level LICENSE file for details.
+##
+## SPDX-License-Identifier: Apache-2.0
+################################################################################
+
+from dataclasses import dataclass, asdict
+from typing import Optional, Literal
+
+
+@dataclass
+class Node:
+    id: str
+    smiles: str
+    label: str
+    hoverInfo: str
+    level: int
+    parentId: Optional[str] = None
+    x: Optional[int] = None
+    y: Optional[int] = None
+    # Properties
+    cost: Optional[float] = None
+    bandgap: Optional[float] = None
+    yield_: Optional[float] = None
+    highlight: Optional[str] = "normal"
+    density: Optional[float] = None
+    sascore: Optional[float] = None
+
+    def json(self):
+        ret = asdict(self)
+        ret["yield"] = ret["yield_"]
+        del ret["yield_"]
+        return ret
+
+
+@dataclass
+class Edge:
+    id: str
+    fromNode: str
+    toNode: str
+    status: Literal["computing", "complete"]
+    label: Optional[str] = None
+
+    def json(self):
+        return asdict(self)
+
+
+@dataclass
+class ModelMessage:
+    message: str
+    smiles: Optional[str]
+
+    def json(self):
+        ret = asdict(self)
+        if self.smiles is None:
+            if "smiles" in ret:
+                del ret["smiles"]
+        return ret
diff --git a/dockerscripts/launch_servers.sh b/dockerscripts/launch_servers.sh
index 16c0dceb..6d60ad93 100644
--- a/dockerscripts/launch_servers.sh
+++ b/dockerscripts/launch_servers.sh
@@ -3,7 +3,7 @@
 . /venv/bin/activate
 
 # Launch main server
-export PYTHONPATH=$PYTHONPATH:/app/charge_backend
+export PYTHONPATH=$PYTHONPATH:/app/charge_backend:/app
 uvicorn --host 0.0.0.0 --port 8001 --workers 8 charge_server:app &
 
 # Wait for server to start up
diff --git a/mock_server.py b/mock_server.py
index 7180f12f..a98d0b23 100644
--- a/mock_server.py
+++ b/mock_server.py
@@ -15,107 +15,17 @@
     * ``custom_query``: Execute custom user query
 """
 
-from fastapi import FastAPI, Request, WebSocket, WebSocketDisconnect
-from fastapi.responses import JSONResponse, HTMLResponse
-from fastapi.staticfiles import StaticFiles
-from fastapi.middleware.cors import CORSMiddleware
+from fastapi import WebSocket, WebSocketDisconnect
 from dataclasses import dataclass, asdict
 import asyncio
 import copy
-import os
 import random
-from typing import Any, Optional, Literal
-import requests
+from typing import Optional
 from datetime import datetime
 from loguru import logger
 from charge_backend.molecule_naming import smiles_to_html
-
-app = FastAPI()
-
-# CORS for development
-app.add_middleware(
-    CORSMiddleware,
-    allow_origins=["*"],
-    allow_credentials=True,
-    allow_methods=["*"],
-    allow_headers=["*"],
-)
-
-if "FLASK_APPDIR" in os.environ:
-    DIST_PATH = os.environ["FLASK_APPDIR"]
-else:
-    DIST_PATH = os.path.join(os.path.dirname(__file__), "flask-app", "dist")
-ASSETS_PATH = os.path.join(DIST_PATH, "assets")
-
-if os.path.exists(ASSETS_PATH):
-    # Serve the frontend
-    app.mount("/assets", StaticFiles(directory=ASSETS_PATH), name="assets")
-    app.mount(
-        "/rdkit", StaticFiles(directory=os.path.join(DIST_PATH, "rdkit")), name="rdkit"
-    )
-
-    @app.get("/")
-    async def root(request: Request):
-        logger.info(f"Request for Web UI received. Headers: {str(request.headers)}")
-        with open(os.path.join(DIST_PATH, "index.html"), "r") as fp:
-            html = fp.read()
-
-        html = html.replace(
-            "<!-- APP CONFIG -->",
-            f"""
-           <script>
-           window.APP_CONFIG = {{
-               WS_SERVER: '{os.getenv("WS_SERVER", "ws://localhost:8001/ws")}',
-               VERSION: '{os.getenv("SERVER_VERSION", "")}'
-           }};
-           </script>""",
-        )
-        return HTMLResponse(html)
-
-
-@dataclass
-class Node:
-    id: str
-    smiles: str
-    label: str
-    hoverInfo: str
-    level: int
-    parentId: Optional[str] = None
-    x: Optional[int] = None
-    y: Optional[int] = None
-    # Properties
-    cost: Optional[float] = None
-    bandgap: Optional[float] = None
-    density: Optional[float] = None
-    yield_: Optional[float] = None
-    highlight: Optional[str] = "normal"
-
-    def json(self):
-        ret = asdict(self)
-        ret["yield"] = ret["yield_"]
-        del ret["yield_"]
-        return ret
-
-
-@dataclass
-class Edge:
-    id: str
-    fromNode: str
-    toNode: str
-    status: Literal["computing", "complete"]
-    label: Optional[str] = None
-
-    def json(self):
-        return asdict(self)
-
-
-@dataclass
-class SidebarMessage:
-    content: str
-    smiles: str
-
-    def json(self):
-        return asdict(self)
+from charge_backend.structures import Node, Edge
+from backend.server import app
 
 
 @dataclass
diff --git a/requirements.txt b/requirements.txt
index d38b8a3c..9091331e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,3 +3,6 @@ uvicorn
 python-multipart
 websockets
 requests
+sqlalchemy[asyncio]
+aiomysql
+pydantic