SeeSAR it is an interactive tool for designing/improving ligands for drug discovery from BioSolve-it, that has been recently updated. Looking through the updates it is clear they have been very receptive to user feedback.

• Solution filter, Finding interesting solutions in larger sets of compounds has become much easier in SeeSAR. Compounds can now be filtered based on any available property – allowing you to easily trim down the compound set to the most interesting subset. As before, you can browse through and sort the remaining table entries to further refine your selection. Properties can be those generated by SeeSAR (such as the Hyde affinity assessment, the torsional strain, TPSA, logP, ...) or alternatively properties loaded from an SD file.
• Joined poses, You can now join the ligands found in the protein structure, compounds loaded from file and compounds newly generated within the SeeSAR editor into one “super” table and now provide quick-links to the previous view of only those from a certain origin. This allows you to see in one table the bound ligand as a reference, the project compounds and your last round of designs. You can then select your favorites from the entire table and export these (for example for an upcoming team meeting).
• Defining the protein, SeeSAR decomposes the contents of a PDB file into chains, small molecules, waters and ions. Until now, users had to accept SeeSAR's default assignments, which is fine in the majority of cases. However, there is no rule without exception, e.g., the peptide inhibitor which is mistaken as a short chain, the small molecule which is actually a co-factor, or the solvent molecule that should be ignored. With this update, SeeSAR allows you to change these default assignments to better handle these exceptional cases, allowing you to categorize a short chain as a bound ligand, or re-assign a co-factor as a permanent part of the protein. You can also eliminate protein elements altogether.
• SMILES, PDB and MOL file support, SeeSAR now comes with with additional molecule readers that broaden the scope of the application. Aside from standard 3D molecule file formats (SDF and mol2), SeeSAR now supports 1D and 2D file formats as well as reading small molecules from PDB format. If no 3D coordinates are given, SeeSAR will calculate a clash-free, low energy conformation on the fly: with the SeeSAR positioning function you can then place such input molecules in the active site of interest. Amongst other things, this feature facilitates the importing of molecules straight from your favourite chemical drawing program and assessing such structures in in the context of your protein of interest.

There is a review of an earlier version of SeeSAR here, and a tutorial showing how to incorporate SeeSAR into a KNIME workflow.