Dear all, I have written some CADD tools, and the details are described below. All of these programs are released under GNU/GPL. You can download them from: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------- CADD tools (linux & irix) pscan_2.2.0 PSCAN is a small but a practical tool for finding any potential binding site of a protein. It can picture the size and appearance of a binding site, and point out the possible pharmacophore.Thus it is helpful for drug design. While running DOCK, QCPE_MS is necessary for autoMS and even the next step sphgen. QCPE_MS, however, is a commercial package. Now, PSCAN and SPHBOX can do the same job. After removing all dots outside of the target binding site by SPDBV (or others), and choosing several positions you are interesting, run SPHBOX to generate sph and box files. pmol2q_2.1.1_rc2 PMOL2Q is a specific file format converter for protein pdb file to mol2 file with adding hydrogens and partial charges. From v2.1.1, PMOL2Q can also output pdbq and pdbqs format. (The pdbqs format is added solvation data according with ADDSOL in AutoDock) It can recognize each amino acid and reconstruct the coordination precisely. The bond length of 109 pm for C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H are used for adding hydrogens.You can choose to add global hydrogens or only polar hydrogens. KOLL and AMBER95 partial charges are available in PMOL2Q. PMOL2Q can also check probabel error of protein coordination, including incomplete atom_missing residues and atom bumps. Hydrogens will not be added on incomplete residues if they exist. You need to fix it by other program before converting file format. (ex. SPDBV can fix the incomplete residues by mutate function) dbfilter_2.2.1 DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-molecular built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Common_atoms_only, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. ----------------------------------------------------------------- 每天都 Yahoo!奇摩 海的顏色、風的氣息、愛你的溫度，盡在信紙底圖 http://tw.promo.yahoo.com/mail_premium/stationery.html