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

scripps.edu

AutoDock
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.

ucsd.edu

Continuity
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
AutoGrow: A Novel Algorithm for Protein Inhibitor Design

Molecular Viewer/Structural Bioinformatics

Biskit
Modular, object-oriented Python library for structural bioinformatics research.
BALLView
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.
MMTK
The Molecular Modelling Toolkit.
Chimera
An extensible molecular modeling system.
Vimes
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
BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology that includes MGLTools.
docking.org
Interesting blogs about ZINC, DOCK and more.
DOVIS
DOcking-based VIrtual Screening.
PyMOL
Molecular visualization system used in many publications.
PocketPicker
Binding Site Prediction plugin for Pymol
Molekel
Molekel is an open-source multiplatform molecular visualization program being developed at the Swiss National Supercomputing Centre (CSCS).
FITTED
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.
TinkerCell
A computer-aided design (CAD) tool for synthetic biology

Visual Programming/Workflow Networks

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

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