VERA Logo

VERA

Virtual Execution and Reaction Architecture

A powerful visual workflow platform for computational chemistry and bioinformatics. 100+ specialized nodes, drag-and-drop interface, integrated scientific engines, and interactive 3D molecular viewers all in one application.

Download VERADocumentationGitHub
100+
Specialized Nodes
15+
Molecular File Formats
20+
Plot Types
8+
ML Algorithms
PLATFORM FEATURES

Everything you need formodern research

VERA combines 100+ specialized nodes with best-in-class computational chemistry and bioinformatics tools in a unified, visual platform.

01

Visual Workflow Canvas

Build complex computational pipelines with 100+ specialized nodes using an intuitive drag-and-drop canvas. Features real-time workflow validation, undo/redo support, node resizing, and automatic connection management.

02

Molecular Docking Suite

Complete AutoDock Vina integration with both CPU and GPU (CUDA) versions. Includes receptor/ligand preparation nodes, grid search optimization, Vina Split, docking analysis, and molecular merging capabilities.

03

GROMACS Molecular Dynamics

Full GROMACS workflow: system preparation, energy minimization, NVT/NPT equilibration, production MD simulations, MDAnalysis for trajectory analysis, CHARMM-GUI input support, XTC extraction, and 3D visualization.

04

Multi-Format Data I/O

Native support for 15+ file formats: molecular (SDF, MOL, MOL2, PDB, PDBQT, XYZ) and data (CSV, Excel, TXT, JSON). Automatic format detection, batch processing, folder I/O nodes, and specialized viewers.

05

Machine Learning Suite

Scikit-learn integration with 8 algorithms: Logistic Regression, Random Forest, SVM/SVR, KNN, Linear Regression. Full model lifecycle (train/test split, save/load, predict) plus K-means, Agglomerative clustering, and PCA.

06

Molecular Visualization

Interactive visualization with 2D structure drawing, 3D molecular viewer (NGL.js Web3DViewer), ProLIF protein-ligand interaction fingerprinting, MD trajectory viewers, and 20+ plot types including scientific charts.

07

Database Connectivity

Direct integration with PubChem compound search and RCSB PDB protein structure retrieval. Automatic data format conversion and batch retrieval support from major chemical databases.

08

Extensible Plugin System

Modular plugin architecture for custom node development. Automatic plugin discovery from plugins folder, dynamic loading/reloading, complete plugin API, and example 'hello_vera' plugin as development template.

09

Project Management

Complete workflow management with .vsw file format. Features recent projects dialog on startup, workflow validation with visual feedback, execution state tracking, and automatic temp file cleanup per session.

10

Cheminformatics Tools

RDKit and OpenBabel engines for molecular processing: structure minimization with force fields (UFF, MMFF94), 3D conformer generation with genetic algorithm (ETKDG), structure validation, and format conversion.

11

DataFrame Operations

Pandas-based data manipulation: Select Columns, Filter Rows by conditions, Slice Rows by index, Drop Duplicates, Sort Rows, and Merge DataFrames with SQL-style joins for complete tabular data analysis.

12

Chromatography Analysis

Specialized chromatography workflow: ChromReader for data import, signal smoothing algorithms, baseline correction, automated peak detection, peak integration for quantification, and interactive ChromViewer.

13

Response Surface Methodology

RSA workflow nodes for experimental optimization: RSA Preparation for design setup, RSA Fitting for response surface model generation, and RSA Surface for 3D visualization of response surfaces.

14

Production-Ready Platform

Built with PySide6 (Qt) for native Windows performance. Features session-based temp directory management, resource compilation system, splash screen with loading progress, and professional distribution. Free under MIT License.

Ready to transform your research workflow?

Join researchers worldwide using VERA to accelerate computational chemistry and bioinformatics.

SCIENTIFIC ENGINES

Integrated tools forevery stage of research

VERA brings together the most powerful computational chemistry and bioinformatics tools in one cohesive platform.

Molecular Docking

8 computational nodes

AutoDock Vina NodeCPU Docking

Standard molecular docking with AutoDock Vina CPU version

AutoDock Vina GPU NodeGPU Accelerated

CUDA-accelerated Vina for high-throughput virtual screening

Receptor PreparationStructure Prep

Automated protein preparation for docking (PDBQT conversion)

Ligand PreparationStructure Prep

Ligand preparation with charge and torsion assignment

Docking AnalysisAnalysis

Parse and analyze docking results with scoring metrics

Vina SplitResult Processing

Split multi-model PDBQT files from docking results

Grid SearchGrid Setup

Define search box parameters for docking simulations

Merge MoleculeStructure Tools

Combine multiple molecular structures into single file

Technical Specifications & Requirements

Built for performance on modern Windows workstations.

Platform
Windows 10/11 (64-bit)
Native Windows application
Memory
8GB RAM minimum
16GB+ recommended
Storage
~14GB installer
14GB+ for engines & data
GPU
NVIDIA GPU optional
CUDA 12.1+ for acceleration

Node Library Snapshot

110+
Total Nodes
8
Docking Nodes
10
MD Nodes
8
ML Algorithms
20+
Plot Types
15+
File Formats
EXAMPLE WORKFLOWS

Ready-to-useworkflow templates

Get started quickly with our comprehensive collection of example workflows. Each includes step-by-step instructions and can be loaded directly into VERA.

2D Molecule Drawing

Beginner

Create and edit molecular structures with interactive 2D drawing tools

Visualization

3D Molecule Viewer

Beginner

Interactive 3D visualization of molecular structures with NGL.js integration

Visualization

Molecular Docking

Intermediate

Protein-ligand docking with AutoDock Vina and result analysis

Docking

CHARMM-GUI Molecular Dynamics

Advanced

Complete molecular dynamics simulation workflow from setup to analysis

MD Simulation

Rdkit Minimisation

Beginner

Molecular structure minimization and energy optimization using RDKit

Cheminformatics

Openbabel Minimisation

Beginner

Structure optimization using OpenBabel force fields

Cheminformatics

Conformer Generation

Intermediate

Generate and analyze molecular conformers for structure-activity studies

Cheminformatics

Dataframe Merge

Beginner

Merge and combine multiple chemical datasets with SQL-style joins

Data Analysis

Drop Duplicate Dataframe

Beginner

Remove duplicate entries from chemical datasets

Data Analysis

Filter by Row Dataframe

Beginner

Filter dataframe rows based on specific criteria and conditions

Data Analysis

Select Column Dataframe

Beginner

Select and manipulate specific dataframe columns

Data Analysis

Short by Row Dataframe

Beginner

Sort dataframe rows by one or more specified columns

Data Analysis

Slice Row Dataframe

Beginner

Slice and extract specific row ranges from dataframes

Data Analysis

General Plotting

Beginner

Create publication-ready plots with matplotlib and seaborn

Data Analysis

Pubchem Scraper

Beginner

Scrape and download molecular data from PubChem database

Data Collection

RCSB PDB Viewer

Beginner

View and analyze protein structures from Protein Data Bank

Structural Biology

Prolif Protein Ligand Interaction

Advanced

Analyze protein-ligand interactions with fingerprint generation

Structural Biology

Need more examples or custom workflows?

Our community is constantly building new workflows. Share yours and discover what others have created on GitHub.

View on GitHubDocumentation
Get Started

Download VERA

VERA is free and open-source under the MIT License. Download the pre-compiled installer for Windows or build from source.

MIT License·Free forever, open source
Open Source·Community driven development
No Registration·Download and use immediately
Recommended

Windows Installer

Complete installer with all scientific engines included. No manual setup required.

  • Full access to all 110+ nodes
  • AutoDock Vina CPU & GPU pre-configured
  • GROMACS full MD suite included
  • RDKit and OpenBabel pre-installed
  • No compilation required
Download Installer
Open Source

Source Code

Access the full source code to build, customize, or contribute to VERA.

  • Full access to source code
  • MIT License free forever
  • Contribute nodes or improvements
  • Developer documentation included
  • Build custom distributions
View Repository

System Requirements

Processor
Intel/AMD x64
2.0 GHz or faster recommended
Memory
8 GB RAM min
16 GB recommended for MD
Storage
50 GB free space
SSD recommended
OS
Windows 10/11 x64
Windows 11 recommended

Need help getting started?

Check the documentation, browse node reference, or ask the community on GitHub Discussions.

Explore FeaturesGitHub Repository
OPEN SOURCE COMMUNITY

Built by thecommunity

VERA is free and open source under the MIT License. Get support, report issues, and contribute through GitHub.

Report an Issue

Found a bug or unexpected behavior? Open an issue on GitHub so the community can help.

Open Issue

Join Discussions

Ask questions, share workflows, and connect with other VERA users in GitHub Discussions.

Start a Discussion

Contribute

VERA is open source under the MIT License. Submit pull requests, add nodes, or improve documentation.

Contributing Guide

Documentation

Browse the full documentation, tutorials, and node reference to get the most out of VERA.

View Docs

Star VERA on GitHub

If VERA helps your research, give it a star on GitHub. It helps others discover the project and motivates continued development.

Star on GitHubBrowse Issues
Documentation

Learn VERA from zero to research

Comprehensive guides, tutorials, and reference documentation for VERA 110+ specialized nodes for computational chemistry and bioinformatics.

Before You Begin

System Requirements

  • Windows 10/11 (64-bit) primary platform
  • 8GB RAM minimum (16GB recommended for MD)
  • 50GB free disk space for data and engines
  • NVIDIA GPU optional (CUDA 12.1+ for Vina GPU)

Software Dependencies

  • Python 3.8+ with PySide6 Qt framework
  • AutoDock Vina (CPU and GPU versions)
  • GROMACS molecular dynamics suite
  • RDKit and OpenBabel cheminformatics
  • Pandas, NumPy, Scikit-learn for data/ML

Sample Data & Resources

  • Protein structures (PDB format) for docking/MD
  • Small molecules (SDF/MOL format) for testing
  • Example workflows (.vsw files) for each engine
  • Test datasets for machine learning nodes
  • Plugin examples (hello_vera) for development

Step-by-Step Guide

Get started with VERA in under an hour

1

Download VERA

Get the latest release from GitHub Releases

~5 min
2

Quick Start Tutorial

Build your first workflow in 10 minutes

~10 min
3

Interface Overview

Master the VERA workspace and panels

~15 min
4

Example Workflows

Explore pre-built workflow templates

~20 min

Getting Started

Getting Started Overview
Complete beginner's guide and learning paths
Installation Guide
Step-by-step installation instructions
Quick Start Tutorial
Your first workflow in 10 minutes
Interface Overview
Understanding the VERA workspace
Example Workflows
Ready-to-use workflow templates

Core Features

Node-Based Workflows
Creating and managing computational workflows
Canvas Operations
Working with the visual workflow editor
Data Management
Handling molecular and experimental data
File I/O Operations
Importing and exporting data files

Scientific Engines

Molecular Docking
AutoDock Vina and Vina GPU integration
Molecular Dynamics
GROMACS simulation workflows
Cheminformatics
RDKit and OpenBabel molecular processing

Advanced Analysis

Machine Learning
8+ ML algorithms and model training
Data Analysis
Data manipulation, statistics, and processing
Data Visualization
20+ chart types and molecular viewers
Developer Resources
Plugin development and API reference

Plugin Development

Plugin Development Guide
Complete guide to creating custom plugins
Plugin Architecture
Understanding plugin system design
Node Implementation
Creating custom node classes
Advanced Topics
UI customization, security, performance

Node Reference

All Node Categories
Complete reference of all 100+ nodes
Molecular Docking
AutoDock Vina CPU/GPU nodes
Molecular Dynamics
GROMACS simulation nodes
Machine Learning
8+ ML algorithms and tools
Data Processing
Data manipulation and analysis
File I/O
19+ file format support

Data & Visualization

Data Processing
Data manipulation and transformation
File Operations
Import/export data in multiple formats
Plotting & Charts
20+ chart types for data visualization
Molecular Visualization
2D/3D molecular structure viewers

Choose Your Learning Path

Different paths for different research interests.

Molecular Docking Path

Master AutoDock Vina for drug discovery and virtual screening

Learning Progression
  1. 1
    Installation & Interface Overview
  2. 2
    AutoDock Vina CPU Docking Basics
  3. 3
    Receptor & Ligand Preparation
  4. 4
    Grid Search & Parameter Optimization
  5. 5
    Docking Results Analysis
  6. 6
    Docking Visualization
  7. 7
    GPU Acceleration & High-throughput Screening

Molecular Dynamics Path

Learn GROMACS for protein simulations and trajectory analysis

Learning Progression
  1. 1
    Installation & System Requirements
  2. 2
    Protein Structure Preparation (pdb2gmx)
  3. 3
    Energy Minimization (Steepest Descent)
  4. 4
    NVT/NPT Equilibration Protocols
  5. 5
    Production MD Runs (mdrun)
  6. 6
    MDAnalysis: RMSD, RMSF, Radius of Gyration
  7. 7
    CHARMM-GUI Integration & Advanced Setup

Machine Learning & Data

Learn Scikit-learn algorithms and data processing workflows

Learning Progression
  1. 1
    Installation & Data Import (15+ formats)
  2. 2
    DataFrame Operations (Select, Filter, Sort, Merge)
  3. 3
    Train-Test Split & Cross-validation
  4. 4
    8 ML Algorithms (RF, SVM, KNN, Logistic Regression)
  5. 5
    Model Evaluation & Statistical Metrics
  6. 6
    Clustering (K-means, Agglomerative) & PCA
  7. 7
    20+ Plot Types for Data Visualization

Cheminformatics Path

Master molecular structure processing and visualization

Learning Progression
  1. 1
    Installation & RDKit/OpenBabel Setup
  2. 2
    Molecular Structure Minimization
  3. 3
    3D Conformer Generation (ETKDG)
  4. 4
    2D Structure Drawing & Analysis
  5. 5
    Interactive 3D Viewer (NGL.js)
  6. 6
    ProLIF Protein-Ligand Interactions
  7. 7
    Molecular Format Conversion

Need more help?

Can't find what you're looking for? The community is here to help.

Ask CommunityReport Issue