Tools

Some useful (free) sites for CADD:

Powerful Molecule Viewers

• Chimera
• Maestro
• AGM Viewer
• COOT (study the crystal coordinates)
  

Ligand Binding Site Finder

• InCaSiteFinder
• Q-SiteFinder
• Pocket Finder
  

Structure Based Molecule Design

• LigBuilder
  

Analytical softwares

• ZINC
• OpenEye
• ChemAxon
  

Docking Softwares

• DOCK
• AUTODOCK
• Docking Server

Molecular Mechanics

• GROMACS
• NAMD
• TINKER

Protein Structure Modelling

• Modeller
  SWISS-MODEL
• Cation-Pi interaction Finder
• WhatIf Homology Modelling Web Server
• Protein Fold recognition at Phyre
• 1Dto3D prediction using HMMSTR/Rosetta
• MMMTree server
• Robetta Protein Server
  

Loop Modelling

• Modloop
• Loopy
• Coda loop server
  

Protein Electrostatics

• Protein Continuum Electrostatics (PCE)
• CHARMM-Gui
  

Model Check/Verification

• Template/Protein Structure Check
• 2D Graphics check (incl. Ramachandran plots)

Small Compound Databases

• PUBCHEM
• ZINC
  

Graphical Tools

• PMG: the Protein Movie Generator

 

This list is far from being complete. Should your tool be published here as well? Please notify us!