Drug Design and Metabolism Sites

Red - Costware  Green- Freeware/Shareware

Program/Site

Brief Description
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 Tools AutoDock Tools is a graphical front end written in python. It works great under linux and can automate most of the autodock processes. It's freely available.  
CADD Some tools to help with docking including pscan to find binding sites in proteins, pmol2q for mol2 to pdb file, dbfilter to find errors in mol2 files, and xlogp patch.
CAESA Large sets of structures are becoming increasingly widespread. Methods of automatically prioritizing these structures are central to the effective application of
structure generation programs to solve practical problems. CAESA (Computer Assisted Estimation of Synthetic Accessibility) is a computer program to automatically rank sets of molecules according to their ease of synthesis. 
DDASL This program utilizes large existing pharmaceutical databases as input for a new type of structure/activity correlation methodology in order to calculate a large set of new and traditional descriptors to create improved Quantitative Structure-Activity Relationship (QSAR) models that characterize and predict important biological responses.
Drug Design Resources This site aim (currently) is to Analyze, Sort, Classify, Organize, Rank, Annotate relevant links dispersed in the cyberspace the deal with drug design.  Not software, just a site that may help point you in the direction you want to go.
eHiTS

Electronic High Throughput Screening for fast, flexible docking of whole or partial structures to target receptors.  Well, that's the hype, you decide.
EON EON is a program that screens databases of molecules for electrostatic similarity to a lead compound.
Flo "Flo" is a molecular modelling program written by Colin McMartin that helps chemist to visualize molecules and aids the design of lead drug compounds.  Flo is very often used in conjunction with the drug design program "Growmol", written by Regine Bohacek. Flo is the front end graphical program that will set up molecules for a drug design run thru Growmol.
GOLPE GOLPE (Generating Optimal Linear PLS Estimations) is the state of the art chemometric toolbox for 3D QSAR. Designed and implemented by the same people using it in practical scientific work, implements everything it is needed to build, validate and interpret 3D QSAR models.
GrowMol GrowMol, generates organic structures that are both spatially and chemically complementary to the target binding site. By "growing" molecules an atom at a time to fill the various nooks and crannies of a binding site, GrowMol can generate structures with exquisite complementary to the host. At each step, the position and type of atom to be added are randomly selected using Boltzmann statistics to bias acceptance toward atoms that can form favorable interactions with the binding site.
MetaSite MetaSite is a computational procedure specially designed to predict the site of metabolism for xenobiotics starting from the 3D structure of a compound (Free to Academic Users).
MIA MIA develops software for chemometric analysis. Specialties here are tools to analyze, manipulate and transform molecular fields. Many of the tools have proven useful in 3D-QSAR, pharmacodynamic optimization, and diverse fields of drug design and development. 
MIPSim MIPSim is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials.  MIPSim can be used as a standalone program for the automatic exploration of biomolecular similarities but it is specially powerful when interfacing to other well-known external programs including GAMESS, GRID, PLS calculations needed for the GOLPE,  GOPENMOL and InsightII.
PARAGON PARAGON is a set of tools for the design of novel biologically active compounds.
PDBbind The PDBbind database, publicly accessible is constructed to provide a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank (PDB). This updated version has binding affinity data (Kd, Ki, & IC50) for over 2,200 protein-ligand complexes released by PDB before 01/01/2005.
PharmTree PharmTree - A drug discovery tool that is totally web based.   PharmTree is a Pharmacophore classifier for biological properties of chemical compounds.
RECON RECON is an algorithm for the rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules, using atomic charge density fragments precomputed from ab initio wavefunctions.
Somfa Somfa is a graphical tool for structure-activity studies on Windows. SOMFA is a new technique for 3D QSAR designed by Peter Winn and Daniel Robinson. The method is very simple and avoids statistical selection procedures such as PLS. All tests so far show it to be as good as other QSAR methods, and better than many. The SOMFA code and executable may be downloaded.
SPROUT SPROUT 4.1 is the fourth generation of the successful, mature de novo ligand design system. The software has proven to be successful for the generation of novel active ligand molecules. One of the most compelling cases of this kind, is the successful design of an HIV protease inhibitors with SPROUT at one of the customer sites already in the mid 90's.
X-Score X-CScore is a "scoring function", which estimates binding free energies for protein-ligand complexes with known 3D structures.  Typically, it is applied to structure-based drug design in combination with molecular docking or de novo structure generation programs.