------------------------------------- SLEUTH Source Code Directory Contents ------------------------------------- This subdirectory contains the Fortran source code for the current version of the SLEUTH program package. The programs contained in this area include: SELECT A simple program that reads EMBL pdb_select files containing lists of PDB files at various sequence similarity cutoffs, and puts out an input file for the ABSTRACT program. ABSTRACT Takes as input a standard Protein Data Bank (PDB) file, and writes a small abstract file containing: PDB four-letter code and compound name, number of amino acids, amino acid sequence in three-letter code, main and side chain dihedral angles, alpha carbon coordinates, secondary structure via the Richards-Kundrot and Kabsch-Sander algorithms, and buried side chain surface area information. SLEUTH Reads a set of PDB abstract files and then allows interactive queries of the abstract database; ie, the user can search for hits based on generalized combinations of sequence pattern, main chain and side chain angles, secondary structure, side chain surface area burial and distances between specified residues. PROFILE Implements David Eisenberg's 3D protein structure profiles (Science, 253, 164-170, 1991, and followup papers). It reads a data matrix of scores for each amino acid type in each environment class. It then takes as input an abstract file for some known 3D structure and asks for an amino acid sequence file to attempt to align to the 3D structure profile. INFOMAKE Builds a data matrix of scores for each amino acid type in each environment class from a set of known protein structures and aligned sequences. The final resulting matrix is used as input to PROFILE. BLASTER A simple utility that takes the output from the NIH network version of BLAST and makes a list of the observed mutations relative to the query sequence for all significant hits found by BLAST. The BLASTER output can be used as auxiliary input to INFOMAKE. ------------------------ A Note about Building the SLEUTH Executables: The code is written in a standard Fortran dialect that should compile unchanged on most machines. Sample scripts to compile, build an object library and link executables are in subdirectories named for machine type (currently /alpha and /sgi). Note the include file sizes.i which contains the master array dimensions used throughout the package. If you are using an SGI workstation and some or all of the executables fail via a segmentation fault, check the limits for your processes by issuing the "limit" command at the C shell prompt. Most SGI machines seem to have these limits set to quite small values for ordinary users. To eliminate the problem issue the commands "limit filesize unlimited", "limit datasize unlimited" and "limit stacksize unlimited". These same commands can also be put in your .cshrc to be run at login time.