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Molecular Viewer/Structural Bioinformatics
Visual Programming/Workflow Networks
Various useful links.

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
AutoDock Vina
AutoDock Vina is a new program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use
PyRx - Virtual Screening Tool
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening form any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx wizard features easy-to-use user interface and chemical spreadsheet like functionality that makes it a valuable tool for Rational Drug Design.

A problem-solving environment for multi-scale modeling and data analysis in bioengineering and physiology. The Continuity client uses DejaVu and ViewerFramework from MGLTools.
AutoGrow: A Novel Algorithm for Protein Inhibitor Design

Molecular Viewer/Structural Bioinformatics

Modular, object-oriented Python library for structural bioinformatics research.
Molecular modeling and visualization application. Uses Qt for GUI and can be compiled with Python support in which case it provides direct access to Python interpreter in the GUI.
The Molecular Modelling Toolkit.
An extensible molecular modeling system.
Visual Interface to Materials Simulation. Uses wxPython and PyOpenGL.
Molecular View
Uses wxPython and VTK.
Docker 1.0
High-throughput molecular docking using free tools: ZINC 8, AutoDockTools 1.5.2 and Docker 1.0
BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology that includes MGLTools.
Interesting blogs about ZINC, DOCK and more.
DOcking-based VIrtual Screening.
Molecular visualization system used in many publications.
Binding Site Prediction plugin for Pymol
Molekel is an open-source multiplatform molecular visualization program being developed at the Swiss National Supercomputing Centre (CSCS).
Flexibility Induced Through Targeted Evolutionary Description (FITTED) aims at improving the accuracy of existing molecule docking software program. It uses a more accurate protein models and is based on a pharmacophore-oriented docking method combined with a genetic algorithm based docking approach.
A computer-aided design (CAD) tool for synthetic biology

Visual Programming/Workflow Networks

Efficient Learning, Large-scale Inference, and Optimization Toolkit for machine learning applications. Uses wxPython.
Component-based data mining software. Uses PyQt.
Python based framework for creation of dataflow networks to build algorithms graphically.
Solve Puzzles for Science

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